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Showing metabocard for PS(DiMe(13,5)/DiMe(13,5)) (HMDB0061572)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2014-04-11 22:07:52 UTC
Update Date2022-11-30 19:11:54 UTC
HMDB IDHMDB0061572
Secondary Accession Numbers
  • HMDB61572
Metabolite Identification
Common NamePS(DiMe(13,5)/DiMe(13,5))
DescriptionPS(DiMe(13,5)/DiMe(13,5)) is a phosphatidylserine (PS or GPSer). It is a glycerophospholipid in which a phosphorylserine moiety occupies a glycerol substitution site. As is the case with diacylglycerols, glycerophosphoserines can have many different combinations of fatty acids of varying lengths and saturation attached at the C-1 and C-2 positions. Fatty acids containing 16, 18 and 20 carbons are the most common. PS(DiMe(13,5)/DiMe(13,5)), in particular, consists of one chain of 14,17-epoxy-15-methyldocosa-14,16-dienoic at the C-1 position and one chain of 14,17-epoxy-15-methyldocosa-14,16-dienoic at the C-2 position. The 14,17-epoxy-15-methyldocosa-14,16-dienoic moiety is derived from fish oil, while the 14,17-epoxy-15-methyldocosa-14,16-dienoic moiety is derived from fish oil. Phosphatidylserine or 1,2-diacyl-sn-glycero-3-phospho-L-serine is distributed widely among animals, plants and microorganisms. It is usually less than 10% of the total phospholipids, the greatest concentration being in myelin from brain tissue. However, it may comprise 10 to 20 mol% of the total phospholipid in the plasma membrane and endoplasmic reticulum of the cell. Phosphatidylserine is an acidic (anionic) phospholipid with three ionizable groups, i.e. the phosphate moiety, the amino group and the carboxyl function. As with other acidic lipids, it exists in nature in salt form, but it has a high propensity to chelate to calcium via the charged oxygen atoms of both the carboxyl and phosphate moieties, modifying the conformation of the polar head group. This interaction may be of considerable relevance to the biological function of phosphatidylserine, especially during bone formation for example. As phosphatidylserine is located entirely on the inner monolayer surface of the plasma membrane (and of other cellular membranes) and it is the most abundant anionic phospholipids. Therefore phosphatidylseriine may make the largest contribution to interfacial effects in membranes involving non-specific electrostatic interactions. This normal distribution is disturbed during platelet activation and cellular apoptosis. In human plasma, 1-stearoyl-2-oleoyl and 1-stearoyl-2-arachidonoyl species predominate, but in brain (especially grey matter), retina and many other tissues 1-stearoyl-2-docosahexaenoyl species are very abundant. Indeed, the ratio of n-3 to n-6 fatty acids in brain phosphatidylserine is very much higher than in most other lipids. While most phospholipids have a saturated fatty acid on C-1 and an unsaturated fatty acid on C-2 of the glycerol backbone, the fatty acid distribution at the C-1 and C-2 positions of glycerol within phospholipids is continually in flux, owing to phospholipid degradation and the continuous phospholipid remodeling that occurs while these molecules are in membranes. Phosphatidylserines typically carry a net charge of -1 at physiological pH. They mostly have palmitic or stearic acid on carbon 1 and a long chain unsaturated fatty acid (e.g. 18:2, 20:4 and 22:6) on carbon 2. PS biosynthesis involves an exchange reaction of serine for ethanolamine in PE.
Structure
Data?1563866205
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0061572 (PS(DiMe(13,5)/DiMe(13,5)))


  Mrv1652303032023542D          

 68 69  0  0  0  0            999 V2000
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M  END
Download

3D MOL for HMDB0061572 (PS(DiMe(13,5)/DiMe(13,5)))

HMDB0061572
     RDKit          3D
PS(DiMe(13,5)/DiMe(13,5))
162163  0  0  0  0  0  0  0  0999 V2000
    1.3886   -1.1135    7.7264 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2788   -1.5523    6.2925 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5538   -2.2007    5.7873 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3078   -2.5988    4.3380 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5097   -3.2514    3.7360 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2269   -3.6375    2.3367 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6326   -3.0606    1.2544 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2229   -3.6417    0.1628 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5430   -3.1959   -1.1983 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4297   -2.5002   -1.9143 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -4.5565   -1.5484   -6.0916 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -5.7498   -0.7632   -4.0985 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9343    0.3366   -3.1287 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3826    1.4275   -3.3172 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7201    0.1416   -2.0021 O   0  0  0  0  0  0  0  0  0  0  0  0
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    7.2223    3.7075    2.3849 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.1296    4.8408    2.6339 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.1803    5.0586    1.6024 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.6159    5.3179    0.2112 C   0  0  0  0  0  0  0  0  0  0  0  0
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    7.5145    2.3615    2.5923 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.7555    1.7398    3.1062 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3386    1.6994    2.2111 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2199    0.2134    2.2734 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4647   -4.7134    0.5626 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7771   -5.7067   -0.3063 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4639   -4.7143    1.9287 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8051   -5.6446    2.8906 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5339   -1.5097    8.3397 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3644   -1.4304    8.2030 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3910   -0.0019    7.8189 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4046   -2.2568    6.2026 H   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D SDF for HMDB0061572 (PS(DiMe(13,5)/DiMe(13,5)))


  Mrv1652303032023542D          

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  2  3  1  0  0  0  0
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  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
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  7  9  1  0  0  0  0
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  9 11  2  0  0  0  0
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 66  6  1  0  0  0  0
 65 54  1  0  0  0  0
 67 31  1  0  0  0  0
 68 37  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0061572

> <DATABASE_NAME>
hmdb

> <SMILES>
CCCCCC1=C(C)C(C)=C(CCCCCCCCCCCCC(=O)OCC(COP(O)(=O)OCC(N)C(O)=O)OC(=O)CCCCCCCCCCCCC2=C(C)C(C)=C(CCCCC)O2)O1

> <INCHI_IDENTIFIER>
InChI=1S/C54H94NO12P/c1-7-9-27-33-48-42(3)44(5)50(66-48)35-29-23-19-15-11-13-17-21-25-31-37-52(56)62-39-46(40-63-68(60,61)64-41-47(55)54(58)59)65-53(57)38-32-26-22-18-14-12-16-20-24-30-36-51-45(6)43(4)49(67-51)34-28-10-8-2/h46-47H,7-41,55H2,1-6H3,(H,58,59)(H,60,61)

> <INCHI_KEY>
FCNURIXTSOPMGD-UHFFFAOYSA-N

> <FORMULA>
C54H94NO12P

> <MOLECULAR_WEIGHT>
980.315

> <EXACT_MASS>
979.651364469

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
162

> <JCHEM_AVERAGE_POLARIZABILITY>
119.40138918355417

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-amino-3-({[2,3-bis({[13-(3,4-dimethyl-5-pentylfuran-2-yl)tridecanoyl]oxy})propoxy](hydroxy)phosphoryl}oxy)propanoic acid

> <ALOGPS_LOGP>
4.69

> <JCHEM_LOGP>
13.956760447747275

> <ALOGPS_LOGS>
-5.61

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
2.1784112376523947

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.4680969050584411

> <JCHEM_PKA_STRONGEST_BASIC>
9.376604467851028

> <JCHEM_POLAR_SURFACE_AREA>
197.95999999999998

> <JCHEM_REFRACTIVITY>
270.8278

> <JCHEM_ROTATABLE_BOND_COUNT>
46

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.43e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-amino-3-{[2,3-bis({[13-(3,4-dimethyl-5-pentylfuran-2-yl)tridecanoyl]oxy})propoxy(hydroxy)phosphoryl]oxy}propanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0061572 (PS(DiMe(13,5)/DiMe(13,5)))

HMDB0061572
     RDKit          3D
PS(DiMe(13,5)/DiMe(13,5))
162163  0  0  0  0  0  0  0  0999 V2000
    1.3886   -1.1135    7.7264 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2788   -1.5523    6.2925 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5538   -2.2007    5.7873 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3078   -2.5988    4.3380 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5097   -3.2514    3.7360 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2269   -3.6375    2.3367 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6326   -3.0606    1.2544 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2229   -3.6417    0.1628 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5430   -3.1959   -1.1983 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4297   -2.5002   -1.9143 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8562   -2.0654   -3.2980 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8647   -1.3643   -4.1211 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6050   -2.1126   -4.4606 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2375   -1.2118   -5.3458 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5443   -1.8461   -5.7742 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2281   -0.8246   -6.6508 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5564   -1.2326   -7.1840 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5565   -1.5484   -6.0916 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7531   -0.3692   -5.1760 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7498   -0.7632   -4.0985 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9343    0.3366   -3.1287 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3826    1.4275   -3.3172 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7201    0.1416   -2.0021 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8752    1.2031   -1.0459 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7543    0.5934    0.0791 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7557    1.6982    1.2174 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4609    1.8566    1.6329 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1845    3.0060    2.8060 P   0  0  0  0  0  5  0  0  0  0  0  0
   -5.3150    2.4553    3.9424 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5571    3.6517    3.5011 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2427    4.2559    2.1030 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0155    5.3804    1.9330 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2338    6.4877    1.2250 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8020    6.0142   -0.0873 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1921    7.6021    1.0395 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5640    7.9249   -0.1203 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6688    8.2764    2.1503 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2917   -0.4854    0.5554 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9850   -1.6335    0.9937 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9134   -2.5257    0.9029 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6876   -2.0974    1.6011 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7132   -2.1179    0.4673 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2927   -2.4937    0.8676 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4950   -2.4406   -0.4224 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0367   -2.7099   -0.2579 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4480   -1.6784    0.7167 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6653   -0.2813    0.2683 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1457    0.7982    1.1576 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3541    0.7945    1.3644 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7482    1.9117    2.2784 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1849    2.0922    2.5632 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0236    2.3770    1.3167 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4248    2.6245    1.8075 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0001    3.8019    1.9293 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.2223    3.7075    2.3849 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.1296    4.8408    2.6339 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.1803    5.0586    1.6024 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.6159    5.3179    0.2112 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.7414    5.5502   -0.7777 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.1659    5.7913   -2.1511 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.5145    2.3615    2.5923 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.7555    1.7398    3.1062 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3386    1.6994    2.2111 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2199    0.2134    2.2734 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4647   -4.7134    0.5626 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7771   -5.7067   -0.3063 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4639   -4.7143    1.9287 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8051   -5.6446    2.8906 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5339   -1.5097    8.3397 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3644   -1.4304    8.2030 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3910   -0.0019    7.8189 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4046   -2.2568    6.2026 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0051   -0.6531    5.6945 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3619   -1.4748    5.8872 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6839   -3.1290    6.3955 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4716   -3.2938    4.3352 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1317   -1.6506    3.7949 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8508   -4.1181    4.3443 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3229   -2.4648    3.7262 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4478   -2.5432   -1.2293 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8426   -4.0948   -1.8095 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.6171   -1.3501 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5837   -3.2048   -2.0469 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7842   -1.4340   -3.1768 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2045   -2.9685   -3.8834 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3554   -1.1389   -5.1163 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6583   -0.3589   -3.6963 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0546   -2.4931   -3.6017 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8864   -2.9755   -5.0966 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3350   -0.8443   -6.2171 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5192   -0.3093   -4.7534 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3569   -2.7442   -6.3568 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0979   -2.0484   -4.8356 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2713    0.1882   -6.1491 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5406   -0.6580   -7.5258 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4482   -2.0610   -7.9037 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9753   -0.3663   -7.7449 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5353   -1.7410   -6.5915 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2983   -2.4173   -5.4789 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7868   -0.1630   -4.6884 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0869    0.5359   -5.7305 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2974   -1.6138   -3.5421 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -4.6850   -1.0508    0.0804 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3526   -3.5381    1.2498 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8892   -1.8113    1.6185 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9838   -3.2282   -1.0725 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7329   -1.4855   -0.9247 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5383   -2.5640   -1.2165 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8607   -3.7009    0.2054 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6674   -1.8540    0.6998 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8774   -1.9044    1.6982 H   0  0  0  0  0  0  0  0  0  0  0  0
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    1.2157    1.7425    3.2441 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3440    2.9652    3.2441 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5958    1.2165    3.1059 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9872    1.5463    0.5906 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6680    3.3216    0.8696 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.5278    5.7792    2.7367 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.5826    4.6932    3.6533 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.8703    4.1776    1.5919 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.8285    5.9240    1.8951 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.0324    4.4658   -0.1498 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.0007    6.2223    0.2689 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.3525    6.4481   -0.4570 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.4662    4.7206   -0.8217 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.8757    6.3763   -2.8125 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.9888    4.8164   -2.6895 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.1790    6.2927   -2.1457 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.5426    1.5816    2.3716 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.4808    0.8275    3.6787 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.1765    2.4313    3.8955 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5040   -0.1528    1.5175 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.2206   -0.2317    2.0103 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0115   -0.1629    3.2957 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6907   -5.5117   -0.2984 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2258   -5.7045   -1.3244 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9344   -6.7240    0.1576 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7404   -5.4097    3.0658 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3760   -5.6589    3.8462 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8454   -6.6961    2.5099 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
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M  END
Download

PDB for HMDB0061572 (PS(DiMe(13,5)/DiMe(13,5)))

HEADER    PROTEIN                                 03-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-MAR-20         0                                  
HETATM    1  C   UNK     0     -15.100 -44.862   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0     -14.474 -43.455   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0     -12.943 -43.294   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0     -12.316 -41.887   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0     -10.785 -41.726   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0     -10.158 -40.319   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0     -10.928 -38.986   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0     -12.460 -38.825   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -9.898 -37.841   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0     -10.218 -36.335   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -8.491 -38.468   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -7.157 -37.698   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -5.824 -38.468   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -4.490 -37.698   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -3.156 -38.468   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -1.822 -37.698   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -0.489 -38.468   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       0.845 -37.698   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       2.179 -38.468   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       3.512 -37.698   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       4.846 -38.468   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       6.180 -37.698   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       7.513 -38.468   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       8.847 -37.698   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0       8.847 -36.158   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0      10.181 -38.468   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0      11.514 -37.698   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      12.848 -38.468   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      12.848 -40.008   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0      14.182 -40.778   0.000  0.00  0.00           O+0
HETATM   31  P   UNK     0      14.182 -42.318   0.000  0.00  0.00           P+0
HETATM   32  O   UNK     0      15.722 -42.318   0.000  0.00  0.00           O+0
HETATM   33  O   UNK     0      14.182 -43.858   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0      12.848 -44.628   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      12.848 -46.168   0.000  0.00  0.00           C+0
HETATM   36  N   UNK     0      11.514 -46.938   0.000  0.00  0.00           N+0
HETATM   37  C   UNK     0      14.182 -46.938   0.000  0.00  0.00           C+0
HETATM   38  O   UNK     0      15.515 -46.168   0.000  0.00  0.00           O+0
HETATM   39  O   UNK     0      14.182 -37.698   0.000  0.00  0.00           O+0
HETATM   40  C   UNK     0      15.515 -38.468   0.000  0.00  0.00           C+0
HETATM   41  O   UNK     0      15.515 -40.008   0.000  0.00  0.00           O+0
HETATM   42  C   UNK     0      16.849 -37.698   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0      18.183 -38.468   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0      19.516 -37.698   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0      20.850 -38.468   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0      22.184 -37.698   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0      23.517 -38.468   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0      24.851 -37.698   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0      26.185 -38.468   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0      27.518 -37.698   0.000  0.00  0.00           C+0
HETATM   51  C   UNK     0      28.852 -38.468   0.000  0.00  0.00           C+0
HETATM   52  C   UNK     0      30.186 -37.698   0.000  0.00  0.00           C+0
HETATM   53  C   UNK     0      31.519 -38.468   0.000  0.00  0.00           C+0
HETATM   54  C   UNK     0      32.853 -37.698   0.000  0.00  0.00           C+0
HETATM   55  C   UNK     0      33.014 -36.166   0.000  0.00  0.00           C+0
HETATM   56  C   UNK     0      31.870 -35.136   0.000  0.00  0.00           C+0
HETATM   57  C   UNK     0      34.520 -35.846   0.000  0.00  0.00           C+0
HETATM   58  C   UNK     0      35.147 -34.439   0.000  0.00  0.00           C+0
HETATM   59  C   UNK     0      35.290 -37.179   0.000  0.00  0.00           C+0
HETATM   60  C   UNK     0      36.822 -37.340   0.000  0.00  0.00           C+0
HETATM   61  C   UNK     0      37.449 -38.747   0.000  0.00  0.00           C+0
HETATM   62  C   UNK     0      38.980 -38.908   0.000  0.00  0.00           C+0
HETATM   63  C   UNK     0      39.606 -40.315   0.000  0.00  0.00           C+0
HETATM   64  C   UNK     0      41.138 -40.476   0.000  0.00  0.00           C+0
HETATM   65  O   UNK     0      34.260 -38.324   0.000  0.00  0.00           O+0
HETATM   66  O   UNK     0      -8.652 -39.999   0.000  0.00  0.00           O+0
HETATM   67  O   UNK     0      12.642 -42.318   0.000  0.00  0.00           O+0
HETATM   68  O   UNK     0      14.182 -48.478   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7   66                                                  
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12   66                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23   25   26                                                  
CONECT   25   24                                                            
CONECT   26   24   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27   29   39                                                  
CONECT   29   28   30                                                       
CONECT   30   29   31                                                       
CONECT   31   30   32   33   67                                             
CONECT   32   31                                                            
CONECT   33   31   34                                                       
CONECT   34   33   35                                                       
CONECT   35   34   36   37                                                  
CONECT   36   35                                                            
CONECT   37   35   38   68                                                  
CONECT   38   37                                                            
CONECT   39   28   40                                                       
CONECT   40   39   41   42                                                  
CONECT   41   40                                                            
CONECT   42   40   43                                                       
CONECT   43   42   44                                                       
CONECT   44   43   45                                                       
CONECT   45   44   46                                                       
CONECT   46   45   47                                                       
CONECT   47   46   48                                                       
CONECT   48   47   49                                                       
CONECT   49   48   50                                                       
CONECT   50   49   51                                                       
CONECT   51   50   52                                                       
CONECT   52   51   53                                                       
CONECT   53   52   54                                                       
CONECT   54   53   55   65                                                  
CONECT   55   54   56   57                                                  
CONECT   56   55                                                            
CONECT   57   55   58   59                                                  
CONECT   58   57                                                            
CONECT   59   57   60   65                                                  
CONECT   60   59   61                                                       
CONECT   61   60   62                                                       
CONECT   62   61   63                                                       
CONECT   63   62   64                                                       
CONECT   64   63                                                            
CONECT   65   59   54                                                       
CONECT   66   11    6                                                       
CONECT   67   31                                                            
CONECT   68   37                                                            
MASTER        0    0    0    0    0    0    0    0   68    0  138    0
END
Download

3D PDB for HMDB0061572 (PS(DiMe(13,5)/DiMe(13,5)))

COMPND    HMDB0061572
HETATM    1  C1  UNL     1       1.389  -1.114   7.726  1.00  0.00           C  
HETATM    2  C2  UNL     1       1.279  -1.552   6.292  1.00  0.00           C  
HETATM    3  C3  UNL     1       2.554  -2.201   5.787  1.00  0.00           C  
HETATM    4  C4  UNL     1       2.308  -2.599   4.338  1.00  0.00           C  
HETATM    5  C5  UNL     1       3.510  -3.251   3.736  1.00  0.00           C  
HETATM    6  C6  UNL     1       3.227  -3.637   2.337  1.00  0.00           C  
HETATM    7  O1  UNL     1       3.633  -3.061   1.254  1.00  0.00           O  
HETATM    8  C7  UNL     1       3.223  -3.642   0.163  1.00  0.00           C  
HETATM    9  C8  UNL     1       3.543  -3.196  -1.198  1.00  0.00           C  
HETATM   10  C9  UNL     1       2.430  -2.500  -1.914  1.00  0.00           C  
HETATM   11  C10 UNL     1       2.856  -2.065  -3.298  1.00  0.00           C  
HETATM   12  C11 UNL     1       1.865  -1.364  -4.121  1.00  0.00           C  
HETATM   13  C12 UNL     1       0.605  -2.113  -4.461  1.00  0.00           C  
HETATM   14  C13 UNL     1      -0.238  -1.212  -5.346  1.00  0.00           C  
HETATM   15  C14 UNL     1      -1.544  -1.846  -5.774  1.00  0.00           C  
HETATM   16  C15 UNL     1      -2.228  -0.825  -6.651  1.00  0.00           C  
HETATM   17  C16 UNL     1      -3.556  -1.233  -7.184  1.00  0.00           C  
HETATM   18  C17 UNL     1      -4.557  -1.548  -6.092  1.00  0.00           C  
HETATM   19  C18 UNL     1      -4.753  -0.369  -5.176  1.00  0.00           C  
HETATM   20  C19 UNL     1      -5.750  -0.763  -4.098  1.00  0.00           C  
HETATM   21  C20 UNL     1      -5.934   0.337  -3.129  1.00  0.00           C  
HETATM   22  O2  UNL     1      -5.383   1.427  -3.317  1.00  0.00           O  
HETATM   23  O3  UNL     1      -6.720   0.142  -2.002  1.00  0.00           O  
HETATM   24  C21 UNL     1      -6.875   1.203  -1.046  1.00  0.00           C  
HETATM   25  C22 UNL     1      -7.754   0.593   0.079  1.00  0.00           C  
HETATM   26  C23 UNL     1      -7.756   1.698   1.217  1.00  0.00           C  
HETATM   27  O4  UNL     1      -6.461   1.857   1.633  1.00  0.00           O  
HETATM   28  P1  UNL     1      -6.185   3.006   2.806  1.00  0.00           P  
HETATM   29  O5  UNL     1      -5.315   2.455   3.942  1.00  0.00           O  
HETATM   30  O6  UNL     1      -7.557   3.652   3.501  1.00  0.00           O  
HETATM   31  O7  UNL     1      -5.243   4.256   2.103  1.00  0.00           O  
HETATM   32  C24 UNL     1      -6.015   5.380   1.933  1.00  0.00           C  
HETATM   33  C25 UNL     1      -5.234   6.488   1.225  1.00  0.00           C  
HETATM   34  N1  UNL     1      -4.802   6.014  -0.087  1.00  0.00           N  
HETATM   35  C26 UNL     1      -6.192   7.602   1.040  1.00  0.00           C  
HETATM   36  O8  UNL     1      -6.564   7.925  -0.120  1.00  0.00           O  
HETATM   37  O9  UNL     1      -6.669   8.276   2.150  1.00  0.00           O  
HETATM   38  O10 UNL     1      -7.292  -0.485   0.555  1.00  0.00           O  
HETATM   39  C27 UNL     1      -6.985  -1.633   0.994  1.00  0.00           C  
HETATM   40  O11 UNL     1      -7.913  -2.526   0.903  1.00  0.00           O  
HETATM   41  C28 UNL     1      -5.688  -2.097   1.601  1.00  0.00           C  
HETATM   42  C29 UNL     1      -4.713  -2.118   0.467  1.00  0.00           C  
HETATM   43  C30 UNL     1      -3.293  -2.494   0.868  1.00  0.00           C  
HETATM   44  C31 UNL     1      -2.495  -2.441  -0.422  1.00  0.00           C  
HETATM   45  C32 UNL     1      -1.037  -2.710  -0.258  1.00  0.00           C  
HETATM   46  C33 UNL     1      -0.448  -1.678   0.717  1.00  0.00           C  
HETATM   47  C34 UNL     1      -0.665  -0.281   0.268  1.00  0.00           C  
HETATM   48  C35 UNL     1      -0.146   0.798   1.158  1.00  0.00           C  
HETATM   49  C36 UNL     1       1.354   0.794   1.364  1.00  0.00           C  
HETATM   50  C37 UNL     1       1.748   1.912   2.278  1.00  0.00           C  
HETATM   51  C38 UNL     1       3.185   2.092   2.563  1.00  0.00           C  
HETATM   52  C39 UNL     1       4.024   2.377   1.317  1.00  0.00           C  
HETATM   53  C40 UNL     1       5.425   2.625   1.808  1.00  0.00           C  
HETATM   54  O12 UNL     1       6.000   3.802   1.929  1.00  0.00           O  
HETATM   55  C41 UNL     1       7.222   3.708   2.385  1.00  0.00           C  
HETATM   56  C42 UNL     1       8.130   4.841   2.634  1.00  0.00           C  
HETATM   57  C43 UNL     1       9.180   5.059   1.602  1.00  0.00           C  
HETATM   58  C44 UNL     1       8.616   5.318   0.211  1.00  0.00           C  
HETATM   59  C45 UNL     1       9.741   5.550  -0.778  1.00  0.00           C  
HETATM   60  C46 UNL     1       9.166   5.791  -2.151  1.00  0.00           C  
HETATM   61  C47 UNL     1       7.514   2.362   2.592  1.00  0.00           C  
HETATM   62  C48 UNL     1       8.755   1.740   3.106  1.00  0.00           C  
HETATM   63  C49 UNL     1       6.339   1.699   2.211  1.00  0.00           C  
HETATM   64  C50 UNL     1       6.220   0.213   2.273  1.00  0.00           C  
HETATM   65  C51 UNL     1       2.465  -4.713   0.563  1.00  0.00           C  
HETATM   66  C52 UNL     1       1.777  -5.707  -0.306  1.00  0.00           C  
HETATM   67  C53 UNL     1       2.464  -4.714   1.929  1.00  0.00           C  
HETATM   68  C54 UNL     1       1.805  -5.645   2.891  1.00  0.00           C  
HETATM   69  H1  UNL     1       0.534  -1.510   8.340  1.00  0.00           H  
HETATM   70  H2  UNL     1       2.364  -1.430   8.203  1.00  0.00           H  
HETATM   71  H3  UNL     1       1.391  -0.002   7.819  1.00  0.00           H  
HETATM   72  H4  UNL     1       0.405  -2.257   6.203  1.00  0.00           H  
HETATM   73  H5  UNL     1       1.005  -0.653   5.695  1.00  0.00           H  
HETATM   74  H6  UNL     1       3.362  -1.475   5.887  1.00  0.00           H  
HETATM   75  H7  UNL     1       2.684  -3.129   6.396  1.00  0.00           H  
HETATM   76  H8  UNL     1       1.472  -3.294   4.335  1.00  0.00           H  
HETATM   77  H9  UNL     1       2.132  -1.651   3.795  1.00  0.00           H  
HETATM   78  H10 UNL     1       3.851  -4.118   4.344  1.00  0.00           H  
HETATM   79  H11 UNL     1       4.323  -2.465   3.726  1.00  0.00           H  
HETATM   80  H12 UNL     1       4.448  -2.543  -1.229  1.00  0.00           H  
HETATM   81  H13 UNL     1       3.843  -4.095  -1.810  1.00  0.00           H  
HETATM   82  H14 UNL     1       2.143  -1.617  -1.350  1.00  0.00           H  
HETATM   83  H15 UNL     1       1.584  -3.205  -2.047  1.00  0.00           H  
HETATM   84  H16 UNL     1       3.784  -1.434  -3.177  1.00  0.00           H  
HETATM   85  H17 UNL     1       3.205  -2.968  -3.883  1.00  0.00           H  
HETATM   86  H18 UNL     1       2.355  -1.139  -5.116  1.00  0.00           H  
HETATM   87  H19 UNL     1       1.658  -0.359  -3.696  1.00  0.00           H  
HETATM   88  H20 UNL     1       0.055  -2.493  -3.602  1.00  0.00           H  
HETATM   89  H21 UNL     1       0.886  -2.975  -5.097  1.00  0.00           H  
HETATM   90  H22 UNL     1       0.335  -0.844  -6.217  1.00  0.00           H  
HETATM   91  H23 UNL     1      -0.519  -0.309  -4.753  1.00  0.00           H  
HETATM   92  H24 UNL     1      -1.357  -2.744  -6.357  1.00  0.00           H  
HETATM   93  H25 UNL     1      -2.098  -2.048  -4.836  1.00  0.00           H  
HETATM   94  H26 UNL     1      -2.271   0.188  -6.149  1.00  0.00           H  
HETATM   95  H27 UNL     1      -1.541  -0.658  -7.526  1.00  0.00           H  
HETATM   96  H28 UNL     1      -3.448  -2.061  -7.904  1.00  0.00           H  
HETATM   97  H29 UNL     1      -3.975  -0.366  -7.745  1.00  0.00           H  
HETATM   98  H30 UNL     1      -5.535  -1.741  -6.591  1.00  0.00           H  
HETATM   99  H31 UNL     1      -4.298  -2.417  -5.479  1.00  0.00           H  
HETATM  100  H32 UNL     1      -3.787  -0.163  -4.688  1.00  0.00           H  
HETATM  101  H33 UNL     1      -5.087   0.536  -5.730  1.00  0.00           H  
HETATM  102  H34 UNL     1      -5.297  -1.614  -3.542  1.00  0.00           H  
HETATM  103  H35 UNL     1      -6.726  -1.075  -4.554  1.00  0.00           H  
HETATM  104  H36 UNL     1      -5.908   1.411  -0.612  1.00  0.00           H  
HETATM  105  H37 UNL     1      -7.442   2.030  -1.452  1.00  0.00           H  
HETATM  106  H38 UNL     1      -8.789   0.614  -0.324  1.00  0.00           H  
HETATM  107  H39 UNL     1      -8.336   1.217   2.022  1.00  0.00           H  
HETATM  108  H40 UNL     1      -8.284   2.556   0.833  1.00  0.00           H  
HETATM  109  H41 UNL     1      -8.034   4.230   2.861  1.00  0.00           H  
HETATM  110  H42 UNL     1      -6.864   5.130   1.273  1.00  0.00           H  
HETATM  111  H43 UNL     1      -6.387   5.801   2.879  1.00  0.00           H  
HETATM  112  H44 UNL     1      -4.376   6.835   1.792  1.00  0.00           H  
HETATM  113  H45 UNL     1      -5.204   6.619  -0.820  1.00  0.00           H  
HETATM  114  H46 UNL     1      -5.154   5.028  -0.224  1.00  0.00           H  
HETATM  115  H47 UNL     1      -6.635   9.296   2.150  1.00  0.00           H  
HETATM  116  H48 UNL     1      -5.856  -3.100   2.042  1.00  0.00           H  
HETATM  117  H49 UNL     1      -5.359  -1.451   2.421  1.00  0.00           H  
HETATM  118  H50 UNL     1      -5.085  -2.756  -0.331  1.00  0.00           H  
HETATM  119  H51 UNL     1      -4.685  -1.051   0.080  1.00  0.00           H  
HETATM  120  H52 UNL     1      -3.353  -3.538   1.250  1.00  0.00           H  
HETATM  121  H53 UNL     1      -2.889  -1.811   1.619  1.00  0.00           H  
HETATM  122  H54 UNL     1      -2.984  -3.228  -1.073  1.00  0.00           H  
HETATM  123  H55 UNL     1      -2.733  -1.485  -0.925  1.00  0.00           H  
HETATM  124  H56 UNL     1      -0.538  -2.564  -1.217  1.00  0.00           H  
HETATM  125  H57 UNL     1      -0.861  -3.701   0.205  1.00  0.00           H  
HETATM  126  H58 UNL     1       0.667  -1.854   0.700  1.00  0.00           H  
HETATM  127  H59 UNL     1      -0.877  -1.904   1.698  1.00  0.00           H  
HETATM  128  H60 UNL     1      -0.284  -0.074  -0.753  1.00  0.00           H  
HETATM  129  H61 UNL     1      -1.788  -0.157   0.157  1.00  0.00           H  
HETATM  130  H62 UNL     1      -0.675   0.835   2.139  1.00  0.00           H  
HETATM  131  H63 UNL     1      -0.344   1.770   0.600  1.00  0.00           H  
HETATM  132  H64 UNL     1       1.805   0.965   0.369  1.00  0.00           H  
HETATM  133  H65 UNL     1       1.724  -0.185   1.715  1.00  0.00           H  
HETATM  134  H66 UNL     1       1.353   2.884   1.906  1.00  0.00           H  
HETATM  135  H67 UNL     1       1.216   1.742   3.244  1.00  0.00           H  
HETATM  136  H68 UNL     1       3.344   2.965   3.244  1.00  0.00           H  
HETATM  137  H69 UNL     1       3.596   1.216   3.106  1.00  0.00           H  
HETATM  138  H70 UNL     1       3.987   1.546   0.591  1.00  0.00           H  
HETATM  139  H71 UNL     1       3.668   3.322   0.870  1.00  0.00           H  
HETATM  140  H72 UNL     1       7.528   5.779   2.737  1.00  0.00           H  
HETATM  141  H73 UNL     1       8.583   4.693   3.653  1.00  0.00           H  
HETATM  142  H74 UNL     1       9.870   4.178   1.592  1.00  0.00           H  
HETATM  143  H75 UNL     1       9.829   5.924   1.895  1.00  0.00           H  
HETATM  144  H76 UNL     1       8.032   4.466  -0.150  1.00  0.00           H  
HETATM  145  H77 UNL     1       8.001   6.222   0.269  1.00  0.00           H  
HETATM  146  H78 UNL     1      10.353   6.448  -0.457  1.00  0.00           H  
HETATM  147  H79 UNL     1      10.466   4.721  -0.822  1.00  0.00           H  
HETATM  148  H80 UNL     1       9.876   6.376  -2.812  1.00  0.00           H  
HETATM  149  H81 UNL     1       8.989   4.816  -2.690  1.00  0.00           H  
HETATM  150  H82 UNL     1       8.179   6.293  -2.146  1.00  0.00           H  
HETATM  151  H83 UNL     1       9.543   1.582   2.372  1.00  0.00           H  
HETATM  152  H84 UNL     1       8.481   0.828   3.679  1.00  0.00           H  
HETATM  153  H85 UNL     1       9.176   2.431   3.895  1.00  0.00           H  
HETATM  154  H86 UNL     1       5.504  -0.153   1.518  1.00  0.00           H  
HETATM  155  H87 UNL     1       7.221  -0.232   2.010  1.00  0.00           H  
HETATM  156  H88 UNL     1       6.011  -0.163   3.296  1.00  0.00           H  
HETATM  157  H89 UNL     1       0.691  -5.512  -0.298  1.00  0.00           H  
HETATM  158  H90 UNL     1       2.226  -5.704  -1.324  1.00  0.00           H  
HETATM  159  H91 UNL     1       1.934  -6.724   0.158  1.00  0.00           H  
HETATM  160  H92 UNL     1       0.740  -5.410   3.066  1.00  0.00           H  
HETATM  161  H93 UNL     1       2.376  -5.659   3.846  1.00  0.00           H  
HETATM  162  H94 UNL     1       1.845  -6.696   2.510  1.00  0.00           H  
CONECT    1    2   69   70   71
CONECT    2    3   72   73
CONECT    3    4   74   75
CONECT    4    5   76   77
CONECT    5    6   78   79
CONECT    6    7   67   67
CONECT    7    8
CONECT    8    9   65   65
CONECT    9   10   80   81
CONECT   10   11   82   83
CONECT   11   12   84   85
CONECT   12   13   86   87
CONECT   13   14   88   89
CONECT   14   15   90   91
CONECT   15   16   92   93
CONECT   16   17   94   95
CONECT   17   18   96   97
CONECT   18   19   98   99
CONECT   19   20  100  101
CONECT   20   21  102  103
CONECT   21   22   22   23
CONECT   23   24
CONECT   24   25  104  105
CONECT   25   26   38  106
CONECT   26   27  107  108
CONECT   27   28
CONECT   28   29   29   30   31
CONECT   30  109
CONECT   31   32
CONECT   32   33  110  111
CONECT   33   34   35  112
CONECT   34  113  114
CONECT   35   36   36   37
CONECT   37  115
CONECT   38   39
CONECT   39   40   40   41
CONECT   41   42  116  117
CONECT   42   43  118  119
CONECT   43   44  120  121
CONECT   44   45  122  123
CONECT   45   46  124  125
CONECT   46   47  126  127
CONECT   47   48  128  129
CONECT   48   49  130  131
CONECT   49   50  132  133
CONECT   50   51  134  135
CONECT   51   52  136  137
CONECT   52   53  138  139
CONECT   53   54   63   63
CONECT   54   55
CONECT   55   56   61   61
CONECT   56   57  140  141
CONECT   57   58  142  143
CONECT   58   59  144  145
CONECT   59   60  146  147
CONECT   60  148  149  150
CONECT   61   62   63
CONECT   62  151  152  153
CONECT   63   64
CONECT   64  154  155  156
CONECT   65   66   67
CONECT   66  157  158  159
CONECT   67   68
CONECT   68  160  161  162
END
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SMILES for HMDB0061572 (PS(DiMe(13,5)/DiMe(13,5)))

CCCCCC1=C(C)C(C)=C(CCCCCCCCCCCCC(=O)OCC(COP(O)(=O)OCC(N)C(O)=O)OC(=O)CCCCCCCCCCCCC2=C(C)C(C)=C(CCCCC)O2)O1
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INCHI for HMDB0061572 (PS(DiMe(13,5)/DiMe(13,5)))

InChI=1S/C54H94NO12P/c1-7-9-27-33-48-42(3)44(5)50(66-48)35-29-23-19-15-11-13-17-21-25-31-37-52(56)62-39-46(40-63-68(60,61)64-41-47(55)54(58)59)65-53(57)38-32-26-22-18-14-12-16-20-24-30-36-51-45(6)43(4)49(67-51)34-28-10-8-2/h46-47H,7-41,55H2,1-6H3,(H,58,59)(H,60,61)
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View in JSmolView Stereo Labels
Synonyms
ValueSource
Phosphatidylserine(13D5/13d5)HMDB
Phosphatidylserine(dime(13,5)/dime(13,5))HMDB
PS(13D5/13D5)HMDB
Chemical FormulaC54H94NO12P
Average Molecular Weight980.315
Monoisotopic Molecular Weight979.651364469
IUPAC Name2-amino-3-({[2,3-bis({[13-(3,4-dimethyl-5-pentylfuran-2-yl)tridecanoyl]oxy})propoxy](hydroxy)phosphoryl}oxy)propanoic acid
Traditional Name2-amino-3-{[2,3-bis({[13-(3,4-dimethyl-5-pentylfuran-2-yl)tridecanoyl]oxy})propoxy(hydroxy)phosphoryl]oxy}propanoic acid
CAS Registry NumberNot Available
SMILES
CCCCCC1=C(C)C(C)=C(CCCCCCCCCCCCC(=O)OCC(COP(O)(=O)OCC(N)C(O)=O)OC(=O)CCCCCCCCCCCCC2=C(C)C(C)=C(CCCCC)O2)O1
InChI Identifier
InChI=1S/C54H94NO12P/c1-7-9-27-33-48-42(3)44(5)50(66-48)35-29-23-19-15-11-13-17-21-25-31-37-52(56)62-39-46(40-63-68(60,61)64-41-47(55)54(58)59)65-53(57)38-32-26-22-18-14-12-16-20-24-30-36-51-45(6)43(4)49(67-51)34-28-10-8-2/h46-47H,7-41,55H2,1-6H3,(H,58,59)(H,60,61)
InChI KeyFCNURIXTSOPMGD-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as phosphatidylserines. These are glycerophosphoserines in which two fatty acids are bonded to the glycerol moiety through ester linkages. As is the case with diacylglycerols, phosphatidylserines can have many different combinations of fatty acids of varying lengths and saturation attached to the C-1 and C-2 positions.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassGlycerophospholipids
Sub ClassGlycerophosphoserines
Direct ParentPhosphatidylserines
Alternative Parents
Substituents
  • Diacyl-glycerol-3-phosphoserine
  • Furanoid fatty acid
  • Alpha-amino acid
  • Alpha-amino acid or derivatives
  • Tricarboxylic acid or derivatives
  • Phosphoethanolamine
  • Fatty acid ester
  • Dialkyl phosphate
  • Organic phosphoric acid derivative
  • Phosphoric acid ester
  • Alkyl phosphate
  • Fatty acyl
  • Heteroaromatic compound
  • Furan
  • Amino acid or derivatives
  • Amino acid
  • Carboxylic acid ester
  • Organoheterocyclic compound
  • Oxacycle
  • Carboxylic acid derivative
  • Carboxylic acid
  • Primary amine
  • Primary aliphatic amine
  • Organic oxide
  • Organopnictogen compound
  • Organic nitrogen compound
  • Organonitrogen compound
  • Organooxygen compound
  • Carbonyl group
  • Amine
  • Organic oxygen compound
  • Hydrocarbon derivative
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effect
Organoleptic effect
Disposition
Biological locationRoute of exposureSource
Process
Naturally occurring process
Role
Biological roleIndustrial application
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.0029 g/LALOGPS
logP4.69ALOGPS
logP13.96ChemAxon
logS-5.6ALOGPS
pKa (Strongest Acidic)1.47ChemAxon
pKa (Strongest Basic)9.38ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count7ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area197.96 ŲChemAxon
Rotatable Bond Count46ChemAxon
Refractivity270.83 m³·mol⁻¹ChemAxon
Polarizability119.4 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+297.79130932474
DeepCCS[M-H]-295.47530932474
DeepCCS[M-2H]-328.88730932474
DeepCCS[M+Na]+303.53230932474
AllCCS[M+H]+300.932859911
AllCCS[M+H-H2O]+301.032859911
AllCCS[M+NH4]+300.832859911
AllCCS[M+Na]+300.732859911
AllCCS[M-H]-291.332859911
AllCCS[M+Na-2H]-298.232859911
AllCCS[M+HCOO]-305.832859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022.8.7 minutes32390414
Predicted by Siyang on May 30, 202238.3297 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20222.77 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid5143.2 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid516.4 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid423.1 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid228.5 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid1177.4 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid1840.2 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid1674.5 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)162.5 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid3870.5 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid1397.6 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid3943.7 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid1392.5 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid835.7 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate352.4 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA508.8 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water10.2 seconds40023050

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PS(DiMe(13,5)/DiMe(13,5)) 10V, Positive-QTOFsplash10-0uxr-9000000106-60932d979b0c307176aa2021-09-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PS(DiMe(13,5)/DiMe(13,5)) 20V, Positive-QTOFsplash10-0udi-9000000002-e939dce87868e3c1a63b2021-09-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PS(DiMe(13,5)/DiMe(13,5)) 40V, Positive-QTOFsplash10-0a4i-1090000113-4a1069bc5ac2b11dd6e52021-09-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PS(DiMe(13,5)/DiMe(13,5)) 10V, Positive-QTOFsplash10-001i-0000000109-a2131f2cce979a3840622021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PS(DiMe(13,5)/DiMe(13,5)) 20V, Positive-QTOFsplash10-000t-0000103916-688cf0ac68c5f7ec05f52021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PS(DiMe(13,5)/DiMe(13,5)) 40V, Positive-QTOFsplash10-0002-0000103911-dd96a1894e9cb9844d232021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PS(DiMe(13,5)/DiMe(13,5)) 10V, Negative-QTOFsplash10-004i-0000000009-b7c4b5ba8d6be97c043e2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PS(DiMe(13,5)/DiMe(13,5)) 20V, Negative-QTOFsplash10-004i-0000000019-8932aa05ff30597ec9222021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PS(DiMe(13,5)/DiMe(13,5)) 40V, Negative-QTOFsplash10-01tc-0106070096-5fe19322a70112e84a192021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PS(DiMe(13,5)/DiMe(13,5)) 10V, Positive-QTOFsplash10-000b-0000000999-a756f868587da90cbeb52021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PS(DiMe(13,5)/DiMe(13,5)) 20V, Positive-QTOFsplash10-000e-0900000999-e8079a4b83ae608204ad2021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PS(DiMe(13,5)/DiMe(13,5)) 40V, Positive-QTOFsplash10-000e-0900000999-e8079a4b83ae608204ad2021-09-25Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Spiteller G: Furan fatty acids: occurrence, synthesis, and reactions. Are furan fatty acids responsible for the cardioprotective effects of a fish diet? Lipids. 2005 Aug;40(8):755-71. [PubMed:16296395 ]
  2. Simons K, Toomre D: Lipid rafts and signal transduction. Nat Rev Mol Cell Biol. 2000 Oct;1(1):31-9. [PubMed:11413487 ]
  3. Watson AD: Thematic review series: systems biology approaches to metabolic and cardiovascular disorders. Lipidomics: a global approach to lipid analysis in biological systems. J Lipid Res. 2006 Oct;47(10):2101-11. Epub 2006 Aug 10. [PubMed:16902246 ]
  4. Sethi JK, Vidal-Puig AJ: Thematic review series: adipocyte biology. Adipose tissue function and plasticity orchestrate nutritional adaptation. J Lipid Res. 2007 Jun;48(6):1253-62. Epub 2007 Mar 20. [PubMed:17374880 ]
  5. Lingwood D, Simons K: Lipid rafts as a membrane-organizing principle. Science. 2010 Jan 1;327(5961):46-50. doi: 10.1126/science.1174621. [PubMed:20044567 ]
  6. Divecha N, Irvine RF: Phospholipid signaling. Cell. 1995 Jan 27;80(2):269-78. [PubMed:7834746 ]
  7. van Engeland M, Nieland LJ, Ramaekers FC, Schutte B, Reutelingsperger CP: Annexin V-affinity assay: a review on an apoptosis detection system based on phosphatidylserine exposure. Cytometry. 1998 Jan 1;31(1):1-9. [PubMed:9450519 ]
  8. Vance JE, Tasseva G: Formation and function of phosphatidylserine and phosphatidylethanolamine in mammalian cells. Biochim Biophys Acta. 2013 Mar;1831(3):543-54. doi: 10.1016/j.bbalip.2012.08.016. Epub 2012 Aug 29. [PubMed:22960354 ]
  9. Cevc, Gregor (1993). Phospholipids Handbook. Marcel Dekker.
  10. Gunstone, Frank D., John L. Harwood, and Albert J. Dijkstra (2007). The lipid handbook with CD-ROM. CRC Press.
  11. Jean E. Vance (2008). Thematic Review Series: Glycerolipids. Phosphatidylserine and phosphatidylethanolamine in mammalian cells: two metabolically related aminophospholipids. The Journal of Lipid Research, 49, 1377-1387..
  12. The AOCS Lipid Library [Link]