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Showing metabocard for PGP(20:4(5Z,8Z,11Z,14Z)/22:5(4Z,7Z,10Z,13Z,16Z)) (HMDB0116486)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2017-09-09 08:17:15 UTC
Update Date2022-11-30 19:26:38 UTC
HMDB IDHMDB0116486
Secondary Accession NumbersNone
Metabolite Identification
Common NamePGP(20:4(5Z,8Z,11Z,14Z)/22:5(4Z,7Z,10Z,13Z,16Z))
DescriptionPGP(20:4(5Z,8Z,11Z,14Z)/22:5(4Z,7Z,10Z,13Z,16Z)) is a phosphatidylglycerophosphate (PGP). It is a glycerophospholipid in which a phosphoglycerol moiety occupies a glycerol substitution site followed by another phosphate moiety. Phosphatidylglycerolphosphate is present at a level of 1-2% in most animal tissues, but it can be the second most abundant phospholipid in lung surfactant (up to 11% of the total). It is well established that the concentration of phosphatidylglycerolphosphate increases during fetal development. Phosphatidylglycerolphosphate may be present in animal tissues merely as a precursor for cardiolipin synthesis. As is the case with diacylglycerols, phosphatidylglycerophosphates can have many different combinations of fatty acids of varying lengths and saturation attached to the C-1 and C-2 positions. Fatty acids containing 16, 18 and 20 carbons are the most common. PGP(20:4(5Z,8Z,11Z,14Z)/22:5(4Z,7Z,10Z,13Z,16Z)), in particular, consists of one chain of arachidonic acid at the C-1 position and one chain of osbond acid at the C-2 position. They are synthesized by the addition of glycerol 3-phosphate to a CDP-diacylglycerol. In turn, PGPs are dephosphorylated to phosphatidylglycerols (PGs). 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.
Structure
Data?1563873722
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0116486 (PGP(20:4(5Z,8Z,11Z,14Z)/22:5(4Z,7Z,10Z,13Z,16Z)))

PGP(20:4(5Z,8Z,11Z,14Z)/22:5(4Z,7Z,10Z,13Z,16Z))
  Mrv1652309171703192D          

 65 64  0  0  1  0            999 V2000
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M  END
Download

3D MOL for HMDB0116486 (PGP(20:4(5Z,8Z,11Z,14Z)/22:5(4Z,7Z,10Z,13Z,16Z)))

HMDB0116486
     RDKit          3D
PGP(20:4(5Z,8Z,11Z,14Z)/22:5(4Z,7Z,10Z,13Z,16Z))
141140  0  0  0  0  0  0  0  0999 V2000
   -5.4582   10.9348    3.7431 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5395    9.9387    4.0789 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0018    8.5422    4.2848 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3425    7.9925    3.0316 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7721    6.5971    3.3097 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1819    6.0576    2.0825 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D SDF for HMDB0116486 (PGP(20:4(5Z,8Z,11Z,14Z)/22:5(4Z,7Z,10Z,13Z,16Z)))

PGP(20:4(5Z,8Z,11Z,14Z)/22:5(4Z,7Z,10Z,13Z,16Z))
  Mrv1652309171703192D          

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M  END
> <DATABASE_ID>
HMDB0116486

> <DATABASE_NAME>
hmdb

> <SMILES>
[H][C@](O)(COP(O)(O)=O)COP(O)(=O)OC[C@@]([H])(COC(=O)CCC\C=C/C\C=C/C\C=C/C\C=C/CCCCC)OC(=O)CC\C=C/C\C=C/C\C=C/C\C=C/C\C=C/CCCCC

> <INCHI_IDENTIFIER>
InChI=1S/C48H78O13P2/c1-3-5-7-9-11-13-15-17-19-21-22-24-26-28-30-32-34-36-38-40-48(51)61-46(44-60-63(55,56)59-42-45(49)41-58-62(52,53)54)43-57-47(50)39-37-35-33-31-29-27-25-23-20-18-16-14-12-10-8-6-4-2/h11-14,17-20,22,24-25,27-28,30-31,33-34,36,45-46,49H,3-10,15-16,21,23,26,29,32,35,37-44H2,1-2H3,(H,55,56)(H2,52,53,54)/b13-11-,14-12-,19-17-,20-18-,24-22-,27-25-,30-28-,33-31-,36-34-/t45-,46+/m0/s1

> <INCHI_KEY>
LXGUZGDAVFGNLL-SRCHOXFBSA-N

> <FORMULA>
C48H78O13P2

> <MOLECULAR_WEIGHT>
925.087

> <EXACT_MASS>
924.491766568

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
141

> <JCHEM_AVERAGE_POLARIZABILITY>
100.74282077943533

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(2S)-3-({[(2R)-2-[(4Z,7Z,10Z,13Z,16Z)-docosa-4,7,10,13,16-pentaenoyloxy]-3-[(5Z,8Z,11Z,14Z)-icosa-5,8,11,14-tetraenoyloxy]propoxy](hydroxy)phosphoryl}oxy)-2-hydroxypropoxy]phosphonic acid

> <ALOGPS_LOGP>
7.65

> <JCHEM_LOGP>
12.001877228000001

> <ALOGPS_LOGS>
-6.07

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-3

> <JCHEM_PKA>
2.040206143663672

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.3548792963908545

> <JCHEM_PKA_STRONGEST_BASIC>
-3.410499386302644

> <JCHEM_POLAR_SURFACE_AREA>
195.34999999999997

> <JCHEM_REFRACTIVITY>
262.24120000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
43

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
7.87e-04 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S)-3-{[(2R)-2-[(4Z,7Z,10Z,13Z,16Z)-docosa-4,7,10,13,16-pentaenoyloxy]-3-[(5Z,8Z,11Z,14Z)-icosa-5,8,11,14-tetraenoyloxy]propoxy(hydroxy)phosphoryl]oxy}-2-hydroxypropoxyphosphonic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0116486 (PGP(20:4(5Z,8Z,11Z,14Z)/22:5(4Z,7Z,10Z,13Z,16Z)))

HMDB0116486
     RDKit          3D
PGP(20:4(5Z,8Z,11Z,14Z)/22:5(4Z,7Z,10Z,13Z,16Z))
141140  0  0  0  0  0  0  0  0999 V2000
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M  END
Download

PDB for HMDB0116486 (PGP(20:4(5Z,8Z,11Z,14Z)/22:5(4Z,7Z,10Z,13Z,16Z)))

HEADER    PROTEIN                                 17-SEP-17   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: PGP(20:4(5Z,8Z,11Z,14Z)/22:5(4Z,7Z,10Z,13Z,16Z))  
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-SEP-17         0                                  
HETATM    1  H   UNK     0       5.198   1.798   0.000  0.00  0.00           H+0
HETATM    2  C   UNK     0      -4.446   0.673   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -5.771   1.436   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      -7.097   0.673   0.000  0.00  0.00           O+0
HETATM    5  H   UNK     0      -3.680  -0.652   0.000  0.00  0.00           H+0
HETATM    6  O   UNK     0      -5.212  -0.652   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      -3.120   1.439   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -1.794   0.673   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       1.487   0.641   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       2.813  -0.124   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.139   0.641   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.465  -0.124   0.000  0.00  0.00           C+0
HETATM   13  P   UNK     0       0.092   1.210   0.000  0.00  0.00           P+0
HETATM   14  O   UNK     0      -0.583   0.039   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       0.092   2.605   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       3.511   1.729   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       6.791   0.641   0.000  0.00  0.00           O+0
HETATM   18  P   UNK     0       8.269   1.037   0.000  0.00  0.00           P+0
HETATM   19  O   UNK     0       8.269   2.568   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       9.748   0.641   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       7.504  -0.289   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0      -8.423   1.436   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      -8.423   2.876   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0      -9.756   0.665   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0     -11.089   1.436   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0     -12.422   0.665   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0     -13.755   1.436   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0     -15.295   1.436   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0     -16.628   0.665   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0     -17.961   1.436   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0     -19.501   1.436   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0     -20.834   0.665   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0     -22.167   1.436   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0     -23.707   1.436   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0     -25.040   0.665   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0     -26.373   1.436   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0     -27.913   1.436   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0     -29.246   0.665   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0     -30.579   1.436   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0     -31.912   0.665   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0     -33.245   1.436   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0     -34.578   0.665   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0      -6.601  -1.436   0.000  0.00  0.00           C+0
HETATM   44  O   UNK     0      -6.601  -2.876   0.000  0.00  0.00           O+0
HETATM   45  C   UNK     0      -7.934  -0.665   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0      -9.267  -1.436   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0     -10.600  -0.665   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0     -12.140  -0.665   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0     -13.473  -1.436   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0     -14.806  -0.665   0.000  0.00  0.00           C+0
HETATM   51  C   UNK     0     -16.346  -0.665   0.000  0.00  0.00           C+0
HETATM   52  C   UNK     0     -17.679  -1.436   0.000  0.00  0.00           C+0
HETATM   53  C   UNK     0     -19.012  -0.665   0.000  0.00  0.00           C+0
HETATM   54  C   UNK     0     -20.552  -0.665   0.000  0.00  0.00           C+0
HETATM   55  C   UNK     0     -21.885  -1.436   0.000  0.00  0.00           C+0
HETATM   56  C   UNK     0     -23.218  -0.665   0.000  0.00  0.00           C+0
HETATM   57  C   UNK     0     -24.758  -0.665   0.000  0.00  0.00           C+0
HETATM   58  C   UNK     0     -26.091  -1.436   0.000  0.00  0.00           C+0
HETATM   59  C   UNK     0     -27.424  -0.665   0.000  0.00  0.00           C+0
HETATM   60  C   UNK     0     -28.964  -0.665   0.000  0.00  0.00           C+0
HETATM   61  C   UNK     0     -30.297  -1.436   0.000  0.00  0.00           C+0
HETATM   62  C   UNK     0     -31.630  -0.665   0.000  0.00  0.00           C+0
HETATM   63  C   UNK     0     -32.963  -1.436   0.000  0.00  0.00           C+0
HETATM   64  C   UNK     0     -34.296  -0.665   0.000  0.00  0.00           C+0
HETATM   65  C   UNK     0     -35.629  -1.436   0.000  0.00  0.00           C+0
CONECT    1   11                                                            
CONECT    2    3    6    5    7                                             
CONECT    3    2    4                                                       
CONECT    4    3   22                                                       
CONECT    5    2                                                            
CONECT    6    2   43                                                       
CONECT    7    2    8                                                       
CONECT    8    7   13                                                       
CONECT    9   10   13                                                       
CONECT   10    9   11                                                       
CONECT   11   10   16    1   12                                             
CONECT   12   11   17                                                       
CONECT   13    9   14   15    8                                             
CONECT   14   13                                                            
CONECT   15   13                                                            
CONECT   16   11                                                            
CONECT   17   12   18                                                       
CONECT   18   17   19   20   21                                             
CONECT   19   18                                                            
CONECT   20   18                                                            
CONECT   21   18                                                            
CONECT   22    4   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27   29                                                       
CONECT   29   28   30                                                       
CONECT   30   29   31                                                       
CONECT   31   30   32                                                       
CONECT   32   31   33                                                       
CONECT   33   32   34                                                       
CONECT   34   33   35                                                       
CONECT   35   34   36                                                       
CONECT   36   35   37                                                       
CONECT   37   36   38                                                       
CONECT   38   37   39                                                       
CONECT   39   38   40                                                       
CONECT   40   39   41                                                       
CONECT   41   40   42                                                       
CONECT   42   41                                                            
CONECT   43    6   44   45                                                  
CONECT   44   43                                                            
CONECT   45   43   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                                                       
CONECT   55   54   56                                                       
CONECT   56   55   57                                                       
CONECT   57   56   58                                                       
CONECT   58   57   59                                                       
CONECT   59   58   60                                                       
CONECT   60   59   61                                                       
CONECT   61   60   62                                                       
CONECT   62   61   63                                                       
CONECT   63   62   64                                                       
CONECT   64   63   65                                                       
CONECT   65   64                                                            
MASTER        0    0    0    0    0    0    0    0   65    0  128    0
END
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3D PDB for HMDB0116486 (PGP(20:4(5Z,8Z,11Z,14Z)/22:5(4Z,7Z,10Z,13Z,16Z)))

COMPND    HMDB0116486
HETATM    1  C1  UNL     1      -5.458  10.935   3.743  1.00  0.00           C  
HETATM    2  C2  UNL     1      -6.540   9.939   4.079  1.00  0.00           C  
HETATM    3  C3  UNL     1      -6.002   8.542   4.285  1.00  0.00           C  
HETATM    4  C4  UNL     1      -5.343   7.992   3.032  1.00  0.00           C  
HETATM    5  C5  UNL     1      -4.772   6.597   3.310  1.00  0.00           C  
HETATM    6  C6  UNL     1      -4.182   6.058   2.083  1.00  0.00           C  
HETATM    7  C7  UNL     1      -2.919   5.751   1.915  1.00  0.00           C  
HETATM    8  C8  UNL     1      -1.928   5.951   3.037  1.00  0.00           C  
HETATM    9  C9  UNL     1      -0.914   6.893   2.435  1.00  0.00           C  
HETATM   10  C10 UNL     1       0.323   6.570   2.354  1.00  0.00           C  
HETATM   11  C11 UNL     1       0.888   5.255   2.844  1.00  0.00           C  
HETATM   12  C12 UNL     1       1.935   5.697   3.833  1.00  0.00           C  
HETATM   13  C13 UNL     1       3.195   5.352   3.730  1.00  0.00           C  
HETATM   14  C14 UNL     1       3.659   4.478   2.622  1.00  0.00           C  
HETATM   15  C15 UNL     1       4.564   5.214   1.722  1.00  0.00           C  
HETATM   16  C16 UNL     1       5.827   4.943   1.514  1.00  0.00           C  
HETATM   17  C17 UNL     1       6.523   3.848   2.174  1.00  0.00           C  
HETATM   18  C18 UNL     1       7.105   2.764   1.422  1.00  0.00           C  
HETATM   19  C19 UNL     1       7.011   2.488   0.165  1.00  0.00           C  
HETATM   20  C20 UNL     1       6.267   3.175  -0.880  1.00  0.00           C  
HETATM   21  C21 UNL     1       5.365   2.189  -1.634  1.00  0.00           C  
HETATM   22  C22 UNL     1       4.512   1.419  -0.742  1.00  0.00           C  
HETATM   23  O1  UNL     1       5.129   0.426  -0.161  1.00  0.00           O  
HETATM   24  O2  UNL     1       3.177   1.582  -0.436  1.00  0.00           O  
HETATM   25  C23 UNL     1       2.538   0.703   0.436  1.00  0.00           C  
HETATM   26  C24 UNL     1       1.323   0.008  -0.098  1.00  0.00           C  
HETATM   27  O3  UNL     1       1.475  -0.838  -1.156  1.00  0.00           O  
HETATM   28  C25 UNL     1       1.904  -0.643  -2.437  1.00  0.00           C  
HETATM   29  O4  UNL     1       2.232   0.495  -2.787  1.00  0.00           O  
HETATM   30  C26 UNL     1       1.945  -1.814  -3.318  1.00  0.00           C  
HETATM   31  C27 UNL     1       2.451  -1.553  -4.716  1.00  0.00           C  
HETATM   32  C28 UNL     1       2.381  -2.943  -5.390  1.00  0.00           C  
HETATM   33  C29 UNL     1       2.861  -2.815  -6.754  1.00  0.00           C  
HETATM   34  C30 UNL     1       2.155  -3.104  -7.799  1.00  0.00           C  
HETATM   35  C31 UNL     1       0.734  -3.612  -7.780  1.00  0.00           C  
HETATM   36  C32 UNL     1       0.734  -4.947  -8.408  1.00  0.00           C  
HETATM   37  C33 UNL     1       0.337  -6.023  -7.805  1.00  0.00           C  
HETATM   38  C34 UNL     1      -0.174  -6.076  -6.423  1.00  0.00           C  
HETATM   39  C35 UNL     1       0.749  -6.923  -5.625  1.00  0.00           C  
HETATM   40  C36 UNL     1       0.427  -8.050  -5.030  1.00  0.00           C  
HETATM   41  C37 UNL     1      -0.863  -8.677  -5.039  1.00  0.00           C  
HETATM   42  C38 UNL     1      -1.631  -8.887  -3.820  1.00  0.00           C  
HETATM   43  C39 UNL     1      -1.415  -8.513  -2.609  1.00  0.00           C  
HETATM   44  C40 UNL     1      -0.302  -7.734  -2.108  1.00  0.00           C  
HETATM   45  C41 UNL     1      -0.857  -6.457  -1.408  1.00  0.00           C  
HETATM   46  C42 UNL     1      -1.669  -5.697  -2.411  1.00  0.00           C  
HETATM   47  C43 UNL     1      -2.288  -4.464  -1.825  1.00  0.00           C  
HETATM   48  C44 UNL     1      -1.292  -3.468  -1.292  1.00  0.00           C  
HETATM   49  C45 UNL     1       2.148   1.315   1.783  1.00  0.00           C  
HETATM   50  O5  UNL     1       1.543   0.315   2.559  1.00  0.00           O  
HETATM   51  P1  UNL     1       1.077   0.796   4.075  1.00  0.00           P  
HETATM   52  O6  UNL     1       1.782   0.019   5.174  1.00  0.00           O  
HETATM   53  O7  UNL     1       1.377   2.430   4.355  1.00  0.00           O  
HETATM   54  O8  UNL     1      -0.595   0.538   4.212  1.00  0.00           O  
HETATM   55  C46 UNL     1      -0.936   0.107   5.488  1.00  0.00           C  
HETATM   56  C47 UNL     1      -2.439  -0.127   5.555  1.00  0.00           C  
HETATM   57  O9  UNL     1      -3.039   1.114   5.258  1.00  0.00           O  
HETATM   58  C48 UNL     1      -2.788  -1.115   4.461  1.00  0.00           C  
HETATM   59  O10 UNL     1      -4.155  -1.296   4.365  1.00  0.00           O  
HETATM   60  P2  UNL     1      -4.560  -2.388   3.158  1.00  0.00           P  
HETATM   61  O11 UNL     1      -5.496  -3.461   3.695  1.00  0.00           O  
HETATM   62  O12 UNL     1      -5.321  -1.619   1.853  1.00  0.00           O  
HETATM   63  O13 UNL     1      -3.147  -3.131   2.577  1.00  0.00           O  
HETATM   64  H1  UNL     1      -5.365  11.699   4.567  1.00  0.00           H  
HETATM   65  H2  UNL     1      -5.672  11.517   2.807  1.00  0.00           H  
HETATM   66  H3  UNL     1      -4.465  10.451   3.671  1.00  0.00           H  
HETATM   67  H4  UNL     1      -7.059  10.245   4.995  1.00  0.00           H  
HETATM   68  H5  UNL     1      -7.297   9.890   3.248  1.00  0.00           H  
HETATM   69  H6  UNL     1      -6.902   7.917   4.546  1.00  0.00           H  
HETATM   70  H7  UNL     1      -5.345   8.498   5.174  1.00  0.00           H  
HETATM   71  H8  UNL     1      -6.122   7.896   2.253  1.00  0.00           H  
HETATM   72  H9  UNL     1      -4.556   8.685   2.715  1.00  0.00           H  
HETATM   73  H10 UNL     1      -4.170   6.630   4.196  1.00  0.00           H  
HETATM   74  H11 UNL     1      -5.707   5.971   3.540  1.00  0.00           H  
HETATM   75  H12 UNL     1      -4.866   5.893   1.217  1.00  0.00           H  
HETATM   76  H13 UNL     1      -2.557   5.352   0.989  1.00  0.00           H  
HETATM   77  H14 UNL     1      -1.540   4.993   3.318  1.00  0.00           H  
HETATM   78  H15 UNL     1      -2.369   6.525   3.877  1.00  0.00           H  
HETATM   79  H16 UNL     1      -1.299   7.867   2.076  1.00  0.00           H  
HETATM   80  H17 UNL     1       1.013   7.304   1.896  1.00  0.00           H  
HETATM   81  H18 UNL     1       1.286   4.798   1.927  1.00  0.00           H  
HETATM   82  H19 UNL     1       0.149   4.616   3.322  1.00  0.00           H  
HETATM   83  H20 UNL     1       1.652   6.334   4.682  1.00  0.00           H  
HETATM   84  H21 UNL     1       3.951   5.690   4.455  1.00  0.00           H  
HETATM   85  H22 UNL     1       4.194   3.589   3.091  1.00  0.00           H  
HETATM   86  H23 UNL     1       2.799   4.047   2.110  1.00  0.00           H  
HETATM   87  H24 UNL     1       4.160   6.092   1.148  1.00  0.00           H  
HETATM   88  H25 UNL     1       6.413   5.606   0.803  1.00  0.00           H  
HETATM   89  H26 UNL     1       6.011   3.508   3.115  1.00  0.00           H  
HETATM   90  H27 UNL     1       7.430   4.411   2.690  1.00  0.00           H  
HETATM   91  H28 UNL     1       7.742   2.040   2.012  1.00  0.00           H  
HETATM   92  H29 UNL     1       7.576   1.584  -0.207  1.00  0.00           H  
HETATM   93  H30 UNL     1       5.649   4.013  -0.653  1.00  0.00           H  
HETATM   94  H31 UNL     1       7.027   3.521  -1.638  1.00  0.00           H  
HETATM   95  H32 UNL     1       5.978   1.556  -2.318  1.00  0.00           H  
HETATM   96  H33 UNL     1       4.729   2.800  -2.302  1.00  0.00           H  
HETATM   97  H34 UNL     1       3.283  -0.103   0.716  1.00  0.00           H  
HETATM   98  H35 UNL     1       0.491   0.773  -0.259  1.00  0.00           H  
HETATM   99  H36 UNL     1       0.940  -0.615   0.771  1.00  0.00           H  
HETATM  100  H37 UNL     1       0.909  -2.272  -3.356  1.00  0.00           H  
HETATM  101  H38 UNL     1       2.576  -2.640  -2.909  1.00  0.00           H  
HETATM  102  H39 UNL     1       3.498  -1.247  -4.693  1.00  0.00           H  
HETATM  103  H40 UNL     1       1.780  -0.853  -5.223  1.00  0.00           H  
HETATM  104  H41 UNL     1       1.384  -3.372  -5.251  1.00  0.00           H  
HETATM  105  H42 UNL     1       3.082  -3.635  -4.845  1.00  0.00           H  
HETATM  106  H43 UNL     1       3.910  -2.444  -6.886  1.00  0.00           H  
HETATM  107  H44 UNL     1       2.643  -2.964  -8.783  1.00  0.00           H  
HETATM  108  H45 UNL     1       0.275  -3.612  -6.815  1.00  0.00           H  
HETATM  109  H46 UNL     1       0.138  -2.893  -8.447  1.00  0.00           H  
HETATM  110  H47 UNL     1       1.087  -5.067  -9.450  1.00  0.00           H  
HETATM  111  H48 UNL     1       0.371  -6.996  -8.338  1.00  0.00           H  
HETATM  112  H49 UNL     1      -1.204  -6.522  -6.508  1.00  0.00           H  
HETATM  113  H50 UNL     1      -0.324  -5.099  -5.949  1.00  0.00           H  
HETATM  114  H51 UNL     1       1.789  -6.549  -5.543  1.00  0.00           H  
HETATM  115  H52 UNL     1       1.274  -8.549  -4.507  1.00  0.00           H  
HETATM  116  H53 UNL     1      -1.573  -8.228  -5.818  1.00  0.00           H  
HETATM  117  H54 UNL     1      -0.675  -9.728  -5.514  1.00  0.00           H  
HETATM  118  H55 UNL     1      -2.591  -9.491  -3.962  1.00  0.00           H  
HETATM  119  H56 UNL     1      -2.169  -8.813  -1.813  1.00  0.00           H  
HETATM  120  H57 UNL     1       0.189  -8.290  -1.272  1.00  0.00           H  
HETATM  121  H58 UNL     1       0.436  -7.368  -2.786  1.00  0.00           H  
HETATM  122  H59 UNL     1      -1.372  -6.717  -0.485  1.00  0.00           H  
HETATM  123  H60 UNL     1       0.043  -5.859  -1.169  1.00  0.00           H  
HETATM  124  H61 UNL     1      -2.481  -6.352  -2.796  1.00  0.00           H  
HETATM  125  H62 UNL     1      -0.972  -5.370  -3.210  1.00  0.00           H  
HETATM  126  H63 UNL     1      -3.040  -4.746  -1.031  1.00  0.00           H  
HETATM  127  H64 UNL     1      -2.910  -3.942  -2.601  1.00  0.00           H  
HETATM  128  H65 UNL     1      -1.759  -2.818  -0.510  1.00  0.00           H  
HETATM  129  H66 UNL     1      -1.053  -2.773  -2.138  1.00  0.00           H  
HETATM  130  H67 UNL     1      -0.401  -3.912  -0.824  1.00  0.00           H  
HETATM  131  H68 UNL     1       1.402   2.123   1.670  1.00  0.00           H  
HETATM  132  H69 UNL     1       3.032   1.649   2.351  1.00  0.00           H  
HETATM  133  H70 UNL     1       1.005   2.754   5.204  1.00  0.00           H  
HETATM  134  H71 UNL     1      -0.610   0.838   6.254  1.00  0.00           H  
HETATM  135  H72 UNL     1      -0.400  -0.842   5.674  1.00  0.00           H  
HETATM  136  H73 UNL     1      -2.770  -0.505   6.518  1.00  0.00           H  
HETATM  137  H74 UNL     1      -3.705   1.021   4.530  1.00  0.00           H  
HETATM  138  H75 UNL     1      -2.435  -0.661   3.515  1.00  0.00           H  
HETATM  139  H76 UNL     1      -2.284  -2.076   4.699  1.00  0.00           H  
HETATM  140  H77 UNL     1      -6.260  -1.955   1.758  1.00  0.00           H  
HETATM  141  H78 UNL     1      -3.135  -4.085   2.798  1.00  0.00           H  
CONECT    1    2   64   65   66
CONECT    2    3   67   68
CONECT    3    4   69   70
CONECT    4    5   71   72
CONECT    5    6   73   74
CONECT    6    7    7   75
CONECT    7    8   76
CONECT    8    9   77   78
CONECT    9   10   10   79
CONECT   10   11   80
CONECT   11   12   81   82
CONECT   12   13   13   83
CONECT   13   14   84
CONECT   14   15   85   86
CONECT   15   16   16   87
CONECT   16   17   88
CONECT   17   18   89   90
CONECT   18   19   19   91
CONECT   19   20   92
CONECT   20   21   93   94
CONECT   21   22   95   96
CONECT   22   23   23   24
CONECT   24   25
CONECT   25   26   49   97
CONECT   26   27   98   99
CONECT   27   28
CONECT   28   29   29   30
CONECT   30   31  100  101
CONECT   31   32  102  103
CONECT   32   33  104  105
CONECT   33   34   34  106
CONECT   34   35  107
CONECT   35   36  108  109
CONECT   36   37   37  110
CONECT   37   38  111
CONECT   38   39  112  113
CONECT   39   40   40  114
CONECT   40   41  115
CONECT   41   42  116  117
CONECT   42   43   43  118
CONECT   43   44  119
CONECT   44   45  120  121
CONECT   45   46  122  123
CONECT   46   47  124  125
CONECT   47   48  126  127
CONECT   48  128  129  130
CONECT   49   50  131  132
CONECT   50   51
CONECT   51   52   52   53   54
CONECT   53  133
CONECT   54   55
CONECT   55   56  134  135
CONECT   56   57   58  136
CONECT   57  137
CONECT   58   59  138  139
CONECT   59   60
CONECT   60   61   61   62   63
CONECT   62  140
CONECT   63  141
END
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SMILES for HMDB0116486 (PGP(20:4(5Z,8Z,11Z,14Z)/22:5(4Z,7Z,10Z,13Z,16Z)))

[H][C@](O)(COP(O)(O)=O)COP(O)(=O)OC[C@@]([H])(COC(=O)CCC\C=C/C\C=C/C\C=C/C\C=C/CCCCC)OC(=O)CC\C=C/C\C=C/C\C=C/C\C=C/C\C=C/CCCCC
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INCHI for HMDB0116486 (PGP(20:4(5Z,8Z,11Z,14Z)/22:5(4Z,7Z,10Z,13Z,16Z)))

InChI=1S/C48H78O13P2/c1-3-5-7-9-11-13-15-17-19-21-22-24-26-28-30-32-34-36-38-40-48(51)61-46(44-60-63(55,56)59-42-45(49)41-58-62(52,53)54)43-57-47(50)39-37-35-33-31-29-27-25-23-20-18-16-14-12-10-8-6-4-2/h11-14,17-20,22,24-25,27-28,30-31,33-34,36,45-46,49H,3-10,15-16,21,23,26,29,32,35,37-44H2,1-2H3,(H,55,56)(H2,52,53,54)/b13-11-,14-12-,19-17-,20-18-,24-22-,27-25-,30-28-,33-31-,36-34-/t45-,46+/m0/s1
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View in JSmolView Stereo Labels
Synonyms
ValueSource
1-Arachidonoyl-2-osbondoyl-sn-glycero-3-phospho-(1'-sn-glycerol-3'-phosphate)HMDB
PGP(20:4/22:5)HMDB
PGP(20:4n6/22:5n6)HMDB
PGP(20:4W6/22:5W6)HMDB
PGP(42:9)HMDB
1-(5Z,8Z,11Z,14Z-Eicosatetraenoyl)-2-(4Z,7Z,10Z,13Z,16Z-docosapentaenoyl)-sn-glycero-3-phospho-(1'-sn-glycerol-3'-phosphate)HMDB
3-sn-Phosphatidyl-1'-sn-glycerol 3'-phosphoric acidHMDB
[(2S)-3-({[(2R)-2-[(4Z,7Z,10Z,13Z,16Z)-docosa-4,7,10,13,16-pentaenoyloxy]-3-[(8Z,11Z,14Z)-icosa-5,8,11,14-tetraenoyloxy]propoxy](hydroxy)phosphoryl}oxy)-2-hydroxypropoxy]phosphonateHMDB
1-arachidonoyl-2-osbondoyl-sn-glycero-3-phospho-(1'-sn-glycerol-3'-phosphate) SMPDB, HMDB
PGP(20:4/22:5) SMPDB, HMDB
PGP(20:4n6/22:5n6) SMPDB, HMDB
PGP(20:4w6/22:5w6) SMPDB, HMDB
PGP(20:4(5Z,8Z,11Z,14Z)/22:5(4Z,7Z,10Z,13Z,16Z))SMPDB
Chemical FormulaC48H78O13P2
Average Molecular Weight925.087
Monoisotopic Molecular Weight924.491766568
IUPAC Name[(2S)-3-({[(2R)-2-[(4Z,7Z,10Z,13Z,16Z)-docosa-4,7,10,13,16-pentaenoyloxy]-3-[(5Z,8Z,11Z,14Z)-icosa-5,8,11,14-tetraenoyloxy]propoxy](hydroxy)phosphoryl}oxy)-2-hydroxypropoxy]phosphonic acid
Traditional Name(2S)-3-{[(2R)-2-[(4Z,7Z,10Z,13Z,16Z)-docosa-4,7,10,13,16-pentaenoyloxy]-3-[(5Z,8Z,11Z,14Z)-icosa-5,8,11,14-tetraenoyloxy]propoxy(hydroxy)phosphoryl]oxy}-2-hydroxypropoxyphosphonic acid
CAS Registry NumberNot Available
SMILES
[H][C@](O)(COP(O)(O)=O)COP(O)(=O)OC[C@@]([H])(COC(=O)CCC\C=C/C\C=C/C\C=C/C\C=C/CCCCC)OC(=O)CC\C=C/C\C=C/C\C=C/C\C=C/C\C=C/CCCCC
InChI Identifier
InChI=1S/C48H78O13P2/c1-3-5-7-9-11-13-15-17-19-21-22-24-26-28-30-32-34-36-38-40-48(51)61-46(44-60-63(55,56)59-42-45(49)41-58-62(52,53)54)43-57-47(50)39-37-35-33-31-29-27-25-23-20-18-16-14-12-10-8-6-4-2/h11-14,17-20,22,24-25,27-28,30-31,33-34,36,45-46,49H,3-10,15-16,21,23,26,29,32,35,37-44H2,1-2H3,(H,55,56)(H2,52,53,54)/b13-11-,14-12-,19-17-,20-18-,24-22-,27-25-,30-28-,33-31-,36-34-/t45-,46+/m0/s1
InChI KeyLXGUZGDAVFGNLL-SRCHOXFBSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as phosphatidylglycerophosphates. These are glycerophosphoglycerophosphates in which two fatty acids are bonded to the 1-glycerol moiety through ester linkages.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassGlycerophospholipids
Sub ClassGlycerophosphoglycerophosphates
Direct ParentPhosphatidylglycerophosphates
Alternative Parents
Substituents
  • Diacylglycerophosphoglycerophosphate
  • Sn-glycerol-3-phosphate
  • Fatty acid ester
  • Monoalkyl phosphate
  • Dialkyl phosphate
  • Dicarboxylic acid or derivatives
  • Organic phosphoric acid derivative
  • Phosphoric acid ester
  • Alkyl phosphate
  • Fatty acyl
  • Secondary alcohol
  • Carboxylic acid ester
  • Carboxylic acid derivative
  • Organooxygen compound
  • Organic oxide
  • Organic oxygen compound
  • Alcohol
  • Carbonyl group
  • Hydrocarbon derivative
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Source
Process
Naturally occurring process
RoleNot Available
Physical Properties
StateSolid
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
logP7.65ALOGPS
logP12ChemAxon
logS-6.1ALOGPS
pKa (Strongest Acidic)1.35ChemAxon
pKa (Strongest Basic)-3.4ChemAxon
Physiological Charge-3ChemAxon
Hydrogen Acceptor Count8ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area195.35 ŲChemAxon
Rotatable Bond Count43ChemAxon
Refractivity262.24 m³·mol⁻¹ChemAxon
Polarizability100.74 ųChemAxon
Number of Rings0ChemAxon
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]+283.61130932474
DeepCCS[M-H]-281.21530932474
DeepCCS[M-2H]-314.24630932474
DeepCCS[M+Na]+289.52430932474
AllCCS[M+H]+307.632859911
AllCCS[M+H-H2O]+307.732859911
AllCCS[M+NH4]+307.532859911
AllCCS[M+Na]+307.532859911
AllCCS[M-H]-311.832859911
AllCCS[M+Na-2H]-319.032859911
AllCCS[M+HCOO]-326.932859911

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, 2022.3.69 minutes32390414
Predicted by Siyang on May 30, 202232.5235 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20222.53 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid5762.2 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid273.2 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid324.0 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid278.7 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid1044.1 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid1927.3 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 Acid1023.0 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)300.7 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid3347.4 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid1380.7 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid2683.2 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid1360.7 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid753.5 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate314.0 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA560.0 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water12.3 seconds40023050

Predicted Kovats Retention Indices

Not Available
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - PGP(20:4(5Z,8Z,11Z,14Z)/22:5(4Z,7Z,10Z,13Z,16Z)) GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-13Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(20:4(5Z,8Z,11Z,14Z)/22:5(4Z,7Z,10Z,13Z,16Z)) 10V, Positive-QTOFsplash10-0bvi-1387036129-0a44a0f5ed61f3d3024a2019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(20:4(5Z,8Z,11Z,14Z)/22:5(4Z,7Z,10Z,13Z,16Z)) 20V, Positive-QTOFsplash10-0bti-3395023212-56fc39046e46727fdaec2019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(20:4(5Z,8Z,11Z,14Z)/22:5(4Z,7Z,10Z,13Z,16Z)) 40V, Positive-QTOFsplash10-0bt9-9377014230-fb0aa040e388031cfb772019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(20:4(5Z,8Z,11Z,14Z)/22:5(4Z,7Z,10Z,13Z,16Z)) 10V, Negative-QTOFsplash10-0fbi-5069011103-6b3afbb7158a321658602019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(20:4(5Z,8Z,11Z,14Z)/22:5(4Z,7Z,10Z,13Z,16Z)) 20V, Negative-QTOFsplash10-0fb9-9032000000-f91f1f8cc4f3838696642019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(20:4(5Z,8Z,11Z,14Z)/22:5(4Z,7Z,10Z,13Z,16Z)) 40V, Negative-QTOFsplash10-004i-9001000000-22796ac01e64a8adcf432019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(20:4(5Z,8Z,11Z,14Z)/22:5(4Z,7Z,10Z,13Z,16Z)) 10V, Positive-QTOFsplash10-004i-2010006197-352f7bb26e70b53ed95a2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(20:4(5Z,8Z,11Z,14Z)/22:5(4Z,7Z,10Z,13Z,16Z)) 20V, Positive-QTOFsplash10-0ab9-1200002920-0aa91334e587b0e8b2842021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(20:4(5Z,8Z,11Z,14Z)/22:5(4Z,7Z,10Z,13Z,16Z)) 40V, Positive-QTOFsplash10-0udi-0192001100-6102165e64c184e21f1e2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(20:4(5Z,8Z,11Z,14Z)/22:5(4Z,7Z,10Z,13Z,16Z)) 10V, Negative-QTOFsplash10-00di-0010000009-006a2a428b1512dc7f0c2021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(20:4(5Z,8Z,11Z,14Z)/22:5(4Z,7Z,10Z,13Z,16Z)) 20V, Negative-QTOFsplash10-0uka-4084149003-0a51c2ff7207e473d5c62021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(20:4(5Z,8Z,11Z,14Z)/22:5(4Z,7Z,10Z,13Z,16Z)) 40V, Negative-QTOFsplash10-0zi1-3091113000-bfbd8ff7d74fe18c07dc2021-09-25Wishart 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 ID74878198
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound131823141
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 ReferencesNot Available