Hmdb loader

Showing metabocard for Lycopene (HMDB0003000)

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enzymes (1) Show 1 protein
Record Information
Version5.0
StatusDetected and Quantified
Creation Date2006-05-22 15:12:25 UTC
Update Date2022-03-07 02:49:17 UTC
HMDB IDHMDB0003000
Secondary Accession Numbers
  • HMDB03000
Metabolite Identification
Common NameLycopene
DescriptionLycopene (molecular formula: C40H56) is a bright red carotenoid pigment. It is a phytochemical found in tomatoes and other red fruits. Lycopene is the most common carotenoid in the human body and is one of the most potent carotenoid antioxidants. Its name is derived from the tomato's species classification, Solanum lycopersicum. Lycopene is a terpene assembled from 8 isoprene units. Lycopene is the most powerful carotenoid quencher of singlet oxygen. Singlet oxygen from ultraviolet light is a primary cause of skin aging (Wikipedia ).
Structure
Data?1582752260
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0003000 (Lycopene)


  Mrv1652309042000272D          

 40 39  0  0  0  0            999 V2000
10012.361610007.4857    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10011.646110007.8977    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10010.932610007.4857    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10010.217210007.8977    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10009.503710007.4857    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10008.788210007.8977    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10008.072710007.4857    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10007.358710007.8977    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10006.643910007.4857    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10005.927110007.8977    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10005.212310007.4857    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10004.497710007.8977    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10003.783010007.4857    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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10001.638810007.8977    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.924010007.4857    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.209410007.8977    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.494510007.4857    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.779910007.8977    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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10015.221510006.6603    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10012.361610006.6603    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1 29  1  0  0  0  0
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  2  3  1  0  0  0  0
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 35 36  2  0  0  0  0
 36 37  1  0  0  0  0
 36 38  1  0  0  0  0
M  END
Download

3D MOL for HMDB0003000 (Lycopene)

HMDB0003000
     RDKit          3D
Lycopene
 96 95  0  0  0  0  0  0  0  0999 V2000
   11.0872   -4.4242    4.0657 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.2613   -3.1862    4.0162 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.9554   -1.8593    4.0979 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.9366   -3.2075    3.9029 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.2809   -4.5494    3.8144 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2479   -4.6655    2.7589 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7382   -4.2963    1.4167 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.8323   -4.9868    0.7498 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1264   -3.3041    0.8028 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4357   -2.7723   -0.5090 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7993   -1.8478   -1.0543 C   0  0  0  0  0  0  0  0  0  0  0  0
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    7.4080   -0.9003   -3.3246 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5450   -0.1484   -2.1084 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0798    0.8371   -3.0387 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8952    1.3777   -2.7924 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2016    2.4134   -3.5353 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7428    3.1832   -4.6520 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9785    2.6934   -3.1390 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0504    3.6552   -3.6502 C   0  0  0  0  0  0  0  0  0  0  0  0
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   10.7305   -1.3282    5.0272 H   0  0  0  0  0  0  0  0  0  0  0  0
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 39 93  1  0
 40 94  1  0
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 40 96  1  0
M  END
Download

3D SDF for HMDB0003000 (Lycopene)


  Mrv1652309042000272D          

 40 39  0  0  0  0            999 V2000
10012.361610007.4857    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10011.646110007.8977    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10010.932610007.4857    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10010.217210007.8977    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10009.503710007.4857    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10008.788210007.8977    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10008.072710007.4857    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10007.358710007.8977    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10006.643910007.4857    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10005.927110007.8977    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10005.212310007.4857    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10004.497710007.8977    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10003.783010007.4857    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10003.068310007.8977    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10002.353410007.4857    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.638810007.8977    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.924010007.4857    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.209410007.8977    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.494510007.4857    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.779910007.8977    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.065110007.4857    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.350510007.8977    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9996.635810007.4857    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.350510008.7224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.209410008.7224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10003.068310008.7224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10005.927110008.7224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10009.503710006.6603    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10013.077110007.8977    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10013.790510007.4857    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10014.506110007.8977    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10015.221510007.4857    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10015.935010007.8977    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10016.650510007.4857    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10017.364010007.8977    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10018.079410007.4857    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10018.797010007.8977    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10018.079410006.6603    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10015.221510006.6603    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10012.361610006.6603    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1 29  1  0  0  0  0
  1 40  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  5 28  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 10 27  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 14 15  1  0  0  0  0
 14 26  1  0  0  0  0
 15 16  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 18 19  1  0  0  0  0
 18 25  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  2  0  0  0  0
 22 23  1  0  0  0  0
 22 24  1  0  0  0  0
 29 30  2  0  0  0  0
 30 31  1  0  0  0  0
 31 32  2  0  0  0  0
 32 33  1  0  0  0  0
 32 39  1  0  0  0  0
 33 34  1  0  0  0  0
 34 35  1  0  0  0  0
 35 36  2  0  0  0  0
 36 37  1  0  0  0  0
 36 38  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0003000

> <DATABASE_NAME>
hmdb

> <SMILES>
CC(C)=CCC\C(C)=C\C=C\C(\C)=C\C=C\C(\C)=C\C=C\C=C(/C)\C=C\C=C(/C)\C=C\C=C(/C)CCC=C(C)C

> <INCHI_IDENTIFIER>
InChI=1S/C40H56/c1-33(2)19-13-23-37(7)27-17-31-39(9)29-15-25-35(5)21-11-12-22-36(6)26-16-30-40(10)32-18-28-38(8)24-14-20-34(3)4/h11-12,15-22,25-32H,13-14,23-24H2,1-10H3/b12-11+,25-15+,26-16+,31-17+,32-18+,35-21+,36-22+,37-27+,38-28+,39-29+,40-30+

> <INCHI_KEY>
OAIJSZIZWZSQBC-GYZMGTAESA-N

> <FORMULA>
C40H56

> <MOLECULAR_WEIGHT>
536.888

> <EXACT_MASS>
536.438201803

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_ATOM_COUNT>
96

> <JCHEM_AVERAGE_POLARIZABILITY>
73.69457447669498

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(6E,8E,10E,12E,14E,16E,18E,20E,22E,24E,26E)-2,6,10,14,19,23,27,31-octamethyldotriaconta-2,6,8,10,12,14,16,18,20,22,24,26,30-tridecaene

> <ALOGPS_LOGP>
9.16

> <JCHEM_LOGP>
11.931831819333333

> <ALOGPS_LOGS>
-6.13

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_POLAR_SURFACE_AREA>
0.0

> <JCHEM_REFRACTIVITY>
197.806

> <JCHEM_ROTATABLE_BOND_COUNT>
16

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.97e-04 g/l

> <JCHEM_TRADITIONAL_IUPAC>
lycopene

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0003000 (Lycopene)

HMDB0003000
     RDKit          3D
Lycopene
 96 95  0  0  0  0  0  0  0  0999 V2000
   11.0872   -4.4242    4.0657 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.2613   -3.1862    4.0162 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.9554   -1.8593    4.0979 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.9366   -3.2075    3.9029 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.2809   -4.5494    3.8144 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2479   -4.6655    2.7589 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7382   -4.2963    1.4167 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.8323   -4.9868    0.7498 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1264   -3.3041    0.8028 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4357   -2.7723   -0.5090 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7993   -1.8478   -1.0543 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5374   -0.9604   -2.1013 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4080   -0.9003   -3.3246 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5450   -0.1484   -2.1084 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0798    0.8371   -3.0387 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8952    1.3777   -2.7924 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2016    2.4134   -3.5353 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7428    3.1832   -4.6520 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9785    2.6934   -3.1390 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0504    3.6552   -3.6502 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1588    3.6619   -3.0825 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2755    4.5103   -3.3682 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4143    4.2269   -2.6396 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2448    3.0364   -1.7113 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4413    5.1629   -2.4772 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5856    5.0237   -1.9032 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7864    4.9632   -1.3220 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3862    3.8225   -0.9873 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7085    2.5517   -1.3020 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5700    3.8414   -0.1361 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.1751    2.6987    0.0905 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.3192    2.5168    0.9030 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.9065    1.3109    0.9868 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.3736    0.2052    0.2180 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.0375    1.1590    1.9501 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.6643    0.0512    2.9420 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.6184   -1.2846    2.2978 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.6398   -2.1427    2.2643 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.3018   -2.0080    2.8696 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.8973   -3.4351    1.5017 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.2057   -4.9066    3.0780 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.1080   -4.1513    4.4885 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.7065   -5.1853    4.7709 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.0362   -2.0312    3.9819 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.7305   -1.3282    5.0272 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.5475   -1.2554    3.2543 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.3471   -2.3219    3.8697 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.7986   -4.7709    4.8194 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.0541   -5.3368    3.6738 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3032   -4.1161    3.0332 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.9455   -5.7796    2.7114 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.7988   -4.5561    1.0714 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.7844   -6.1030    0.9766 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.7562   -4.8993   -0.3449 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2977   -2.8524    1.4014 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.2223   -3.1293   -1.1550 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9280   -1.6045   -0.1567 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.6774   -1.9100   -3.6991 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.3204   -0.3227   -3.0448 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.8579   -0.3590   -4.1019 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9308   -0.1893   -1.1428 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5886    1.1740   -3.8909 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4017    0.9768   -1.8788 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9464    3.7716   -5.1876 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1673    2.4895   -5.4135 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5285    3.9227   -4.3859 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6654    2.0572   -2.2732 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2009    4.3708   -4.4197 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2296    2.8796   -2.3077 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3816    5.3188   -4.0460 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9842    2.1343   -2.2438 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1503    2.9128   -1.1303 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4353    3.3907   -0.9812 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4838    6.1346   -3.0097 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3242    6.2862   -1.3261 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4840    5.8344   -1.0684 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4901    1.8320   -1.6950 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0752    2.6787   -2.2391 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1944    2.0796   -0.4828 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9895    4.7177    0.3297 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7386    1.8111   -0.3772 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.7584    3.3129    1.4878 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.1091    0.6223   -0.8193 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.1346   -0.5979    0.0378 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.4147   -0.1471    0.6130 H   0  0  0  0  0  0  0  0  0  0  0  0
  -11.9107    0.8039    1.3467 H   0  0  0  0  0  0  0  0  0  0  0  0
  -11.3060    2.0466    2.5013 H   0  0  0  0  0  0  0  0  0  0  0  0
  -11.2760    0.0501    3.8574 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.5954    0.2399    3.2957 H   0  0  0  0  0  0  0  0  0  0  0  0
  -11.5652   -1.5659    1.7820 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5134   -1.8620    2.0594 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2050   -1.2110    3.5977 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0009   -3.0330    3.2680 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.6011   -3.2902    0.6681 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.2317   -4.2327    2.1843 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.9076   -3.7242    1.0250 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  2  3
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  7  9  2  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 12 13  1  0
 12 14  2  0
 14 15  1  0
 15 16  2  0
 16 17  1  0
 17 18  1  0
 17 19  2  0
 19 20  1  0
 20 21  2  0
 21 22  1  0
 22 23  2  0
 23 24  1  0
 23 25  1  0
 25 26  2  0
 26 27  1  0
 27 28  2  0
 28 29  1  0
 28 30  1  0
 30 31  2  0
 31 32  1  0
 32 33  2  0
 33 34  1  0
 33 35  1  0
 35 36  1  0
 36 37  1  0
 37 38  2  3
 38 39  1  0
 38 40  1  0
  1 41  1  0
  1 42  1  0
  1 43  1  0
  3 44  1  0
  3 45  1  0
  3 46  1  0
  4 47  1  0
  5 48  1  0
  5 49  1  0
  6 50  1  0
  6 51  1  0
  8 52  1  0
  8 53  1  0
  8 54  1  0
  9 55  1  0
 10 56  1  0
 11 57  1  0
 13 58  1  0
 13 59  1  0
 13 60  1  0
 14 61  1  0
 15 62  1  0
 16 63  1  0
 18 64  1  0
 18 65  1  0
 18 66  1  0
 19 67  1  0
 20 68  1  0
 21 69  1  0
 22 70  1  0
 24 71  1  0
 24 72  1  0
 24 73  1  0
 25 74  1  0
 26 75  1  0
 27 76  1  0
 29 77  1  0
 29 78  1  0
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 30 80  1  0
 31 81  1  0
 32 82  1  0
 34 83  1  0
 34 84  1  0
 34 85  1  0
 35 86  1  0
 35 87  1  0
 36 88  1  0
 36 89  1  0
 37 90  1  0
 39 91  1  0
 39 92  1  0
 39 93  1  0
 40 94  1  0
 40 95  1  0
 40 96  1  0
M  END
Download

PDB for HMDB0003000 (Lycopene)

HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-20         0                                  
HETATM    1  C   UNK     0    8689.7428680.640   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0    8688.4068681.409   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0    8687.0748680.640   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0    8685.7398681.409   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0    8684.4078680.640   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0    8683.0718681.409   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0    8681.7368680.640   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0    8680.4038681.409   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0    8679.0698680.640   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0    8677.7318681.409   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0    8676.3968680.640   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0    8675.0628681.409   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0    8673.7288680.640   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0    8672.3948681.409   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0    8671.0608680.640   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0    8669.7268681.409   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0    8668.3918680.640   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0    8667.0588681.409   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0    8665.7238680.640   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0    8664.3898681.409   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0    8663.0558680.640   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0    8661.7218681.409   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0    8660.3878680.640   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0    8661.7218682.948   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0    8667.0588682.948   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0    8672.3948682.948   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0    8677.7318682.948   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0    8684.4078679.099   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0    8691.0778681.409   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0    8692.4098680.640   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0    8693.7458681.409   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0    8695.0808680.640   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0    8696.4128681.409   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0    8697.7488680.640   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0    8699.0798681.409   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0    8700.4158680.640   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0    8701.7548681.409   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0    8700.4158679.099   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0    8695.0808679.099   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0    8689.7428679.099   0.000  0.00  0.00           C+0
CONECT    1    2   29   40                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6   28                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   27                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   26                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19   25                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22                                                            
CONECT   25   18                                                            
CONECT   26   14                                                            
CONECT   27   10                                                            
CONECT   28    5                                                            
CONECT   29    1   30                                                       
CONECT   30   29   31                                                       
CONECT   31   30   32                                                       
CONECT   32   31   33   39                                                  
CONECT   33   32   34                                                       
CONECT   34   33   35                                                       
CONECT   35   34   36                                                       
CONECT   36   35   37   38                                                  
CONECT   37   36                                                            
CONECT   38   36                                                            
CONECT   39   32                                                            
CONECT   40    1                                                            
MASTER        0    0    0    0    0    0    0    0   40    0   78    0
END
Download

3D PDB for HMDB0003000 (Lycopene)

COMPND    HMDB0003000
HETATM    1  C1  UNL     1      11.087  -4.424   4.066  1.00  0.00           C  
HETATM    2  C2  UNL     1      10.261  -3.186   4.016  1.00  0.00           C  
HETATM    3  C3  UNL     1      10.955  -1.859   4.098  1.00  0.00           C  
HETATM    4  C4  UNL     1       8.937  -3.207   3.903  1.00  0.00           C  
HETATM    5  C5  UNL     1       8.281  -4.549   3.814  1.00  0.00           C  
HETATM    6  C6  UNL     1       7.248  -4.666   2.759  1.00  0.00           C  
HETATM    7  C7  UNL     1       7.738  -4.296   1.417  1.00  0.00           C  
HETATM    8  C8  UNL     1       8.832  -4.987   0.750  1.00  0.00           C  
HETATM    9  C9  UNL     1       7.126  -3.304   0.803  1.00  0.00           C  
HETATM   10  C10 UNL     1       7.436  -2.772  -0.509  1.00  0.00           C  
HETATM   11  C11 UNL     1       6.799  -1.848  -1.054  1.00  0.00           C  
HETATM   12  C12 UNL     1       6.537  -0.960  -2.101  1.00  0.00           C  
HETATM   13  C13 UNL     1       7.408  -0.900  -3.325  1.00  0.00           C  
HETATM   14  C14 UNL     1       5.545  -0.148  -2.108  1.00  0.00           C  
HETATM   15  C15 UNL     1       5.080   0.837  -3.039  1.00  0.00           C  
HETATM   16  C16 UNL     1       3.895   1.378  -2.792  1.00  0.00           C  
HETATM   17  C17 UNL     1       3.202   2.413  -3.535  1.00  0.00           C  
HETATM   18  C18 UNL     1       3.743   3.183  -4.652  1.00  0.00           C  
HETATM   19  C19 UNL     1       1.979   2.693  -3.139  1.00  0.00           C  
HETATM   20  C20 UNL     1       1.050   3.655  -3.650  1.00  0.00           C  
HETATM   21  C21 UNL     1      -0.159   3.662  -3.083  1.00  0.00           C  
HETATM   22  C22 UNL     1      -1.276   4.510  -3.368  1.00  0.00           C  
HETATM   23  C23 UNL     1      -2.414   4.227  -2.640  1.00  0.00           C  
HETATM   24  C24 UNL     1      -2.245   3.036  -1.711  1.00  0.00           C  
HETATM   25  C25 UNL     1      -3.441   5.163  -2.477  1.00  0.00           C  
HETATM   26  C26 UNL     1      -4.586   5.024  -1.903  1.00  0.00           C  
HETATM   27  C27 UNL     1      -5.786   4.963  -1.322  1.00  0.00           C  
HETATM   28  C28 UNL     1      -6.386   3.823  -0.987  1.00  0.00           C  
HETATM   29  C29 UNL     1      -5.708   2.552  -1.302  1.00  0.00           C  
HETATM   30  C30 UNL     1      -7.570   3.841  -0.136  1.00  0.00           C  
HETATM   31  C31 UNL     1      -8.175   2.699   0.090  1.00  0.00           C  
HETATM   32  C32 UNL     1      -9.319   2.517   0.903  1.00  0.00           C  
HETATM   33  C33 UNL     1      -9.907   1.311   0.987  1.00  0.00           C  
HETATM   34  C34 UNL     1      -9.374   0.205   0.218  1.00  0.00           C  
HETATM   35  C35 UNL     1     -11.038   1.159   1.950  1.00  0.00           C  
HETATM   36  C36 UNL     1     -10.664   0.051   2.942  1.00  0.00           C  
HETATM   37  C37 UNL     1     -10.618  -1.285   2.298  1.00  0.00           C  
HETATM   38  C38 UNL     1      -9.640  -2.143   2.264  1.00  0.00           C  
HETATM   39  C39 UNL     1      -8.302  -2.008   2.870  1.00  0.00           C  
HETATM   40  C40 UNL     1      -9.897  -3.435   1.502  1.00  0.00           C  
HETATM   41  H1  UNL     1      11.206  -4.907   3.078  1.00  0.00           H  
HETATM   42  H2  UNL     1      12.108  -4.151   4.488  1.00  0.00           H  
HETATM   43  H3  UNL     1      10.706  -5.185   4.771  1.00  0.00           H  
HETATM   44  H4  UNL     1      12.036  -2.031   3.982  1.00  0.00           H  
HETATM   45  H5  UNL     1      10.730  -1.328   5.027  1.00  0.00           H  
HETATM   46  H6  UNL     1      10.547  -1.255   3.254  1.00  0.00           H  
HETATM   47  H7  UNL     1       8.347  -2.322   3.870  1.00  0.00           H  
HETATM   48  H8  UNL     1       7.799  -4.771   4.819  1.00  0.00           H  
HETATM   49  H9  UNL     1       9.054  -5.337   3.674  1.00  0.00           H  
HETATM   50  H10 UNL     1       6.303  -4.116   3.033  1.00  0.00           H  
HETATM   51  H11 UNL     1       6.946  -5.780   2.711  1.00  0.00           H  
HETATM   52  H12 UNL     1       9.799  -4.556   1.071  1.00  0.00           H  
HETATM   53  H13 UNL     1       8.784  -6.103   0.977  1.00  0.00           H  
HETATM   54  H14 UNL     1       8.756  -4.899  -0.345  1.00  0.00           H  
HETATM   55  H15 UNL     1       6.298  -2.852   1.401  1.00  0.00           H  
HETATM   56  H16 UNL     1       8.222  -3.129  -1.155  1.00  0.00           H  
HETATM   57  H17 UNL     1       5.928  -1.604  -0.157  1.00  0.00           H  
HETATM   58  H18 UNL     1       7.677  -1.910  -3.699  1.00  0.00           H  
HETATM   59  H19 UNL     1       8.320  -0.323  -3.045  1.00  0.00           H  
HETATM   60  H20 UNL     1       6.858  -0.359  -4.102  1.00  0.00           H  
HETATM   61  H21 UNL     1       4.931  -0.189  -1.143  1.00  0.00           H  
HETATM   62  H22 UNL     1       5.589   1.174  -3.891  1.00  0.00           H  
HETATM   63  H23 UNL     1       3.402   0.977  -1.879  1.00  0.00           H  
HETATM   64  H24 UNL     1       2.946   3.772  -5.188  1.00  0.00           H  
HETATM   65  H25 UNL     1       4.167   2.489  -5.414  1.00  0.00           H  
HETATM   66  H26 UNL     1       4.529   3.923  -4.386  1.00  0.00           H  
HETATM   67  H27 UNL     1       1.665   2.057  -2.273  1.00  0.00           H  
HETATM   68  H28 UNL     1       1.201   4.371  -4.420  1.00  0.00           H  
HETATM   69  H29 UNL     1      -0.230   2.880  -2.308  1.00  0.00           H  
HETATM   70  H30 UNL     1      -1.382   5.319  -4.046  1.00  0.00           H  
HETATM   71  H31 UNL     1      -1.984   2.134  -2.244  1.00  0.00           H  
HETATM   72  H32 UNL     1      -3.150   2.913  -1.130  1.00  0.00           H  
HETATM   73  H33 UNL     1      -1.435   3.391  -0.981  1.00  0.00           H  
HETATM   74  H34 UNL     1      -3.484   6.135  -3.010  1.00  0.00           H  
HETATM   75  H35 UNL     1      -4.324   6.286  -1.326  1.00  0.00           H  
HETATM   76  H36 UNL     1      -6.484   5.834  -1.068  1.00  0.00           H  
HETATM   77  H37 UNL     1      -6.490   1.832  -1.695  1.00  0.00           H  
HETATM   78  H38 UNL     1      -5.075   2.679  -2.239  1.00  0.00           H  
HETATM   79  H39 UNL     1      -5.194   2.080  -0.483  1.00  0.00           H  
HETATM   80  H40 UNL     1      -7.989   4.718   0.330  1.00  0.00           H  
HETATM   81  H41 UNL     1      -7.739   1.811  -0.377  1.00  0.00           H  
HETATM   82  H42 UNL     1      -9.758   3.313   1.488  1.00  0.00           H  
HETATM   83  H43 UNL     1      -9.109   0.622  -0.819  1.00  0.00           H  
HETATM   84  H44 UNL     1     -10.135  -0.598   0.038  1.00  0.00           H  
HETATM   85  H45 UNL     1      -8.415  -0.147   0.613  1.00  0.00           H  
HETATM   86  H46 UNL     1     -11.911   0.804   1.347  1.00  0.00           H  
HETATM   87  H47 UNL     1     -11.306   2.047   2.501  1.00  0.00           H  
HETATM   88  H48 UNL     1     -11.276   0.050   3.857  1.00  0.00           H  
HETATM   89  H49 UNL     1      -9.595   0.240   3.296  1.00  0.00           H  
HETATM   90  H50 UNL     1     -11.565  -1.566   1.782  1.00  0.00           H  
HETATM   91  H51 UNL     1      -7.513  -1.862   2.059  1.00  0.00           H  
HETATM   92  H52 UNL     1      -8.205  -1.211   3.598  1.00  0.00           H  
HETATM   93  H53 UNL     1      -8.001  -3.033   3.268  1.00  0.00           H  
HETATM   94  H54 UNL     1     -10.601  -3.290   0.668  1.00  0.00           H  
HETATM   95  H55 UNL     1     -10.232  -4.233   2.184  1.00  0.00           H  
HETATM   96  H56 UNL     1      -8.908  -3.724   1.025  1.00  0.00           H  
CONECT    1    2   41   42   43
CONECT    2    3    4    4
CONECT    3   44   45   46
CONECT    4    5   47
CONECT    5    6   48   49
CONECT    6    7   50   51
CONECT    7    8    9    9
CONECT    8   52   53   54
CONECT    9   10   55
CONECT   10   11   11   56
CONECT   11   12   57
CONECT   12   13   14   14
CONECT   13   58   59   60
CONECT   14   15   61
CONECT   15   16   16   62
CONECT   16   17   63
CONECT   17   18   19   19
CONECT   18   64   65   66
CONECT   19   20   67
CONECT   20   21   21   68
CONECT   21   22   69
CONECT   22   23   23   70
CONECT   23   24   25
CONECT   24   71   72   73
CONECT   25   26   26   74
CONECT   26   27   75
CONECT   27   28   28   76
CONECT   28   29   30
CONECT   29   77   78   79
CONECT   30   31   31   80
CONECT   31   32   81
CONECT   32   33   33   82
CONECT   33   34   35
CONECT   34   83   84   85
CONECT   35   36   86   87
CONECT   36   37   88   89
CONECT   37   38   38   90
CONECT   38   39   40
CONECT   39   91   92   93
CONECT   40   94   95   96
END
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SMILES for HMDB0003000 (Lycopene)

CC(C)=CCC\C(C)=C\C=C\C(\C)=C\C=C\C(\C)=C\C=C\C=C(/C)\C=C\C=C(/C)\C=C\C=C(/C)CCC=C(C)C
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INCHI for HMDB0003000 (Lycopene)

InChI=1S/C40H56/c1-33(2)19-13-23-37(7)27-17-31-39(9)29-15-25-35(5)21-11-12-22-36(6)26-16-30-40(10)32-18-28-38(8)24-14-20-34(3)4/h11-12,15-22,25-32H,13-14,23-24H2,1-10H3/b12-11+,25-15+,26-16+,31-17+,32-18+,35-21+,36-22+,37-27+,38-28+,39-29+,40-30+
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View in JSmolView Stereo Labels
Synonyms
ValueSource
(6E,8E,10E,12E,14E,16E,18E,20E,22E,24E,26E)-2,6,10,14,19,23,27,31-Octamethyldotriaconta-2,6,8,10,12,14,16,18,20,22,24,26,30-tridecaeneChEBI
all-trans-LycopeneChEBI
all trans LycopeneMeSH
LYC O matoMeSH
Pro-lycopeneMeSH
LYCOMATOMeSH
Pro lycopeneMeSH
(6E,8E,10E,12E,14E,16E,18E,20E,22E,24E,26E)-2,6,10,14,19,23,27,31-Octamethyl-2,6,8,10,12,14,16,18,20,22,24,26,30-dotriacontatridecaeneHMDB
(all-e)-2,6,10,14,19,23,27,31-Octamethyl-2,6,8,10,12,14,16,18,20,22,24,26,30-dotriacontatridecaeneHMDB
trans-LycopeneHMDB
(all-E)-LycopeneHMDB
LycopeneHMDB
psi,psi-CaroteneHMDB
ψ,ψ-CaroteneHMDB
Chemical FormulaC40H56
Average Molecular Weight536.888
Monoisotopic Molecular Weight536.438201803
IUPAC Name(6E,8E,10E,12E,14E,16E,18E,20E,22E,24E,26E)-2,6,10,14,19,23,27,31-octamethyldotriaconta-2,6,8,10,12,14,16,18,20,22,24,26,30-tridecaene
Traditional Namelycopene
CAS Registry Number502-65-8
SMILES
CC(C)=CCC\C(C)=C\C=C\C(\C)=C\C=C\C(\C)=C\C=C\C=C(/C)\C=C\C=C(/C)\C=C\C=C(/C)CCC=C(C)C
InChI Identifier
InChI=1S/C40H56/c1-33(2)19-13-23-37(7)27-17-31-39(9)29-15-25-35(5)21-11-12-22-36(6)26-16-30-40(10)32-18-28-38(8)24-14-20-34(3)4/h11-12,15-22,25-32H,13-14,23-24H2,1-10H3/b12-11+,25-15+,26-16+,31-17+,32-18+,35-21+,36-22+,37-27+,38-28+,39-29+,40-30+
InChI KeyOAIJSZIZWZSQBC-GYZMGTAESA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as carotenes. These are a type of unsaturated hydrocarbons containing eight consecutive isoprene units. They are characterized by the presence of two end-groups (mostly cyclohexene rings, but also cyclopentene rings or acyclic groups) linked by a long branched alkyl chain. Carotenes belonging form a subgroup of the carotenoids family.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassPrenol lipids
Sub ClassTetraterpenoids
Direct ParentCarotenes
Alternative Parents
Substituents
  • Carotene
  • Branched unsaturated hydrocarbon
  • Unsaturated aliphatic hydrocarbon
  • Unsaturated hydrocarbon
  • Olefin
  • Acyclic olefin
  • Hydrocarbon
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationRoute of exposureSource
Process
Naturally occurring process
Role
Industrial applicationBiological role
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point175 °CNot Available
Boiling Point660.90 °C. @ 760.00 mm Hg (est)The Good Scents Company Information System
Water Solubility1.0e-13 mg/L @ 25 °C (est)The Good Scents Company Information System
LogP15.190 (est)The Good Scents Company Information System
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.0004 g/LALOGPS
logP9.16ALOGPS
logP11.93ChemAxon
logS-6.1ALOGPS
Physiological Charge0ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count16ChemAxon
Refractivity197.81 m³·mol⁻¹ChemAxon
Polarizability73.69 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
DarkChem[M+H]+247.58231661259
DarkChem[M-H]-249.92431661259
DeepCCS[M+H]+247.40430932474
DeepCCS[M-H]-245.50930932474
DeepCCS[M-2H]-278.74930932474
DeepCCS[M+Na]+253.01930932474
AllCCS[M+H]+237.032859911
AllCCS[M+H-H2O]+235.432859911
AllCCS[M+NH4]+238.632859911
AllCCS[M+Na]+239.032859911
AllCCS[M-H]-228.332859911
AllCCS[M+Na-2H]-230.232859911
AllCCS[M+HCOO]-232.432859911

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. Predicted by Afia on May 17, 2022.3.13 minutes32390414
Predicted by Siyang on May 30, 202250.6123 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20221.31 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid6453.2 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid1515.0 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid591.2 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid1014.2 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid590.8 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid1915.3 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 Acid1227.7 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)144.2 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid4383.6 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid1573.7 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid2194.7 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid1754.9 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid1079.7 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate590.6 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA1340.8 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water10.9 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
LycopeneCC(C)=CCC\C(C)=C\C=C\C(\C)=C\C=C\C(\C)=C\C=C\C=C(/C)\C=C\C=C(/C)\C=C\C=C(/C)CCC=C(C)C5089.1Standard polar33892256
LycopeneCC(C)=CCC\C(C)=C\C=C\C(\C)=C\C=C\C(\C)=C\C=C\C=C(/C)\C=C\C=C(/C)\C=C\C=C(/C)CCC=C(C)C4285.6Standard non polar33892256
LycopeneCC(C)=CCC\C(C)=C\C=C\C(\C)=C\C=C\C(\C)=C\C=C\C=C(/C)\C=C\C=C(/C)\C=C\C=C(/C)CCC=C(C)C3938.3Semi standard non polar33892256
Spectra
Biological Properties
Cellular Locations
  • Extracellular
  • Membrane (predicted from logP)
Biospecimen Locations
  • Blood
  • Breast Milk
Tissue Locations
  • Adipose Tissue
  • Adrenal Gland
  • Epidermis
  • Fibroblasts
  • Intestine
  • Kidney
  • Leukocyte
  • Liver
  • Pancreas
  • Platelet
  • Prostate
  • Spleen
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified0.177 uMChildren (1-13 years old)FemaleNormal details
BloodDetected and Quantified0.590 +/- 0.220 uMAdolescent (13-18 years old)FemaleNormal details
BloodDetected and Quantified0.585 +/- 0.338 uMAdult (>18 years old)FemaleNormal details
BloodDetected and Quantified0.563 +/- 0.231 uMAdult (>18 years old)FemaleNormal details
BloodDetected and Quantified0.531 +/- 0.237 uMAdult (>18 years old)FemaleNormal details
BloodDetected and Quantified0.527 +/- 0.237 uMAdult (>18 years old)FemaleNormal details
BloodDetected and Quantified0.434 +/- 0.186 uMAdult (>18 years old)FemaleNormal details
BloodDetected and Quantified0.320 +/- 0.120 uMAdult (>18 years old)FemaleNormal details
BloodDetected and Quantified1.24 uMAdult (>18 years old)FemaleNormal details
BloodDetected and Quantified0.771 uMAdult (>18 years old)FemaleNormal details
BloodDetected and Quantified0.71 uMAdult (>18 years old)FemaleNormal details
BloodDetected and Quantified0.51 uMAdult (>18 years old)FemaleNormal details
BloodDetected and Quantified0.631 +/- 0.371 uMAdult (>18 years old)FemaleNormal details
BloodDetected and Quantified0.169 uMAdolescent (13-18 years old)FemaleNormal details
BloodDetected and Quantified1.560 +/- 0.640 uMAdult (>18 years old)BothNormal details
BloodDetected and Quantified1.340 +/- 0.750 uMAdult (>18 years old)BothNormal details
BloodDetected and Quantified0.695 +/- 0.274 uMAdult (>18 years old)BothNormal details
BloodDetected and Quantified0.630 +/- 0.280 uMAdult (>18 years old)BothNormal details
BloodDetected and Quantified0.576 +/- 0.309 uMAdult (>18 years old)BothNormal details
BloodDetected and Quantified0.335 +/- 0.164 uMAdult (>18 years old)BothNormal details
BloodDetected and Quantified0.170 +/- 0.120 uMAdult (>18 years old)BothNormal details
BloodDetected and Quantified0.623 uMAdult (>18 years old)BothNormal details
BloodDetected and Quantified0.567 uMAdult (>18 years old)BothNormal details
BloodDetected and Quantified0.406 uMAdult (>18 years old)BothNormal details
BloodDetected and Quantified0.579 +/- 0.253 uMAdult (>18 years old)MaleNormal details
BloodDetected and Quantified0.730 +/- 0.400 uMChildren (1 - 13 years old)Not SpecifiedNormal details
BloodDetected and Quantified204.884 +/- 93.129 uMAdult (>18 years old)MaleNormal details
BloodDetected and Quantified930 +/- 350 uMAdult (>18 years old)MaleNormal details
BloodDetected and Quantified817.675 +/- 375.684 uMAdult (>18 years old)MaleNormal details
BloodDetected and Quantified1060 +/- 410 uMAdult (>18 years old)MaleNormal details
BloodDetected and Quantified0.820 +/- 0.380 uMAdult (>18 years old)MaleNormal details
BloodDetected and Quantified0.746 +/- 0.379 uMAdult (>18 years old)MaleNormal details
BloodDetected and Quantified0.630 +/- 0.276 uMAdult (>18 years old)MaleNormal details
BloodDetected and Quantified0.622 +/- 0.320 uMAdult (>18 years old)MaleNormal details
BloodDetected and Quantified0.620 +/- 0.308 uMAdult (>18 years old)MaleNormal details
BloodDetected and Quantified0.610 +/- 0.240 uMAdolescent (13-18 years old)MaleNormal details
BloodDetected and Quantified0.01 (0.008-0.014) uMAdult (>18 years old)FemaleNormal details
BloodDetected and Quantified0.505 +/- 0.183 uMAdult (>18 years old)MaleNormal details
BloodDetected and Quantified0.501 +/- 0.338 uMAdult (>18 years old)MaleNormal details
BloodDetected and Quantified1.44 uMAdult (>18 years old)MaleNormal details
BloodDetected and Quantified0.74 uMAdult (>18 years old)MaleNormal details
BloodDetected and Quantified0.5 uMAdult (>18 years old)MaleNormal details
BloodDetected and Quantified0.187 uMChildren (1-13 years old)MaleNormal details
BloodDetected and Quantified0.159 uMAdolescent (13-18 years old)MaleNormal details
BloodDetected and Quantified242.136 +/- 111.755 uMAdult (>18 years old)FemaleNormal details
BloodDetected and Quantified759.376 +/- 318.688 uMAdult (>18 years old)FemaleNormal details
BloodDetected and Quantified0.760 +/- 0.320 uMAdult (>18 years old)FemaleNormal details
BloodDetected and Quantified0.658 +/- 0.341 uMAdult (>18 years old)FemaleNormal details
BloodDetected and Quantified0.330 +/- 0.230 uMAdult (>18 years old)Female
Normal		 details
BloodDetected and Quantified0.394 +/- 0.202 uMAdult (>18 years old)Female
Normal		 details
BloodDetected and Quantified0.248 +/- 0.121 uMAdult (>18 years old)Female
Normal		 details
BloodDetected and Quantified0.374 +/- 0.139 uMAdult (>18 years old)Female
Normal		 details
BloodDetected and Quantified0.926 +/- 0.270 uMAdult (>18 years old)Not Specified
Normal		 details
BloodDetected and Quantified0.640 +/- 0.380 uMAdult (>18 years old)Male
Normal		 details
BloodDetected and Quantified0.510 +/- 0.340 uMAdult (>18 years old)Male
Normal		 details
BloodDetected and Quantified0.474 +/- 0.560 uMAdult (>18 years old)Male
Normal		 details
BloodDetected and Quantified0.440 +/- 0.280 uMAdult (>18 years old)Male
Normal		 details
BloodDetected and Quantified0.703 +/- 0.860 uMAdult (>18 years old)Female
Normal		 details
BloodDetected and Quantified0.610 +/- 0.360 uMAdult (>18 years old)Female
Normal		 details
BloodDetected and Quantified0.350 +/- 0.250 uMAdult (>18 years old)Female
Normal		 details
BloodDetected and Quantified0.143 uMAdult (>18 years old)BothNormal details
BloodDetected and Quantified0.420 +/- 0.320 uMAdult (>18 years old)Both
Normal		 details
BloodDetected and Quantified0.420 +/- 0.280 uMAdult (>18 years old)Both
Normal		 details
BloodDetected and Quantified0.400 +/- 0.280 uMAdult (>18 years old)Both
Normal		 details
BloodDetected and Quantified0.360 +/- 0.240 uMAdult (>18 years old)Both
Normal		 details
BloodDetected and Quantified0.656 +/- 0.0100 uMAdult (>18 years old)Female
Normal		 details
BloodDetected and Quantified0.402 uMAdult (>18 years old)Both
Normal		 details
BloodDetected and Quantified0.61 uMAdult (>18 years old)Both
Normal		 details
BloodDetected and Quantified0.6 uMAdult (>18 years old)Both
Normal		 details
BloodDetected and Quantified0.52 +/- 0.17 uMAdult (>18 years old)BothNormal details
BloodDetected and Quantified0.34 +/- 0.12 uMAdult (>18 years old)BothNormal details
BloodDetected and Quantified0.743 +/- 0.168 uMAdult (>18 years old)Female
Normal		 details
BloodDetected and Quantified0.640 +/- 0.260 uMAdult (>18 years old)Female
Normal		 details
BloodDetected and Quantified0.263 uMAdult (>18 years old)BothNormal details
BloodDetected and Quantified0.0705 uMAdult (>18 years old)BothNormal details
BloodDetected and Quantified0.76 uMAdult (>18 years old)Female
Normal		 details
BloodDetected and Quantified0.68 uMAdult (>18 years old)Female
Normal		 details
BloodDetected and Quantified0.64 uMAdult (>18 years old)Female
Normal		 details
BloodDetected and Quantified0.87 uMAdult (>18 years old)Female
Normal		 details
BloodDetected and Quantified0.707 uMAdult (>18 years old)Female
Normal		 details
BloodDetected and Quantified0.509 uMAdult (>18 years old)Female
Normal		 details
BloodDetected and Quantified0.392 uMAdult (>18 years old)Both
Normal		 details
BloodDetected and Quantified0.59 uMAdult (>18 years old)Both
Normal		 details
BloodDetected and Quantified0.57 uMAdult (>18 years old)Both
Normal		 details
BloodDetected and Quantified0.696 +/- 0.342 uMAdult (>18 years old)Both
Normal		 details
BloodDetected and Quantified0.580 +/- 0.310 uMAdult (>18 years old)Male
Normal		 details
BloodDetected and Quantified0.600 +/- 0.360 uMAdult (>18 years old)Female
Normal		 details
BloodDetected and Quantified0.574 +/- 0.264 uMAdult (>18 years old)Both
Normal		 details
BloodDetected and Quantified580 +/- 240 uMAdult (>18 years old)Female
Normal		 details
BloodDetected and Quantified0.67 uMAdult (>18 years old)Male
Normal		 details
BloodDetected and Quantified0.61 uMAdult (>18 years old)Female
Normal		 details
BloodDetected and Quantified0.280 +/- 0.110 uMAdult (>18 years old)Female
Normal		 details
BloodDetected and Quantified0.260 +/- 0.110 uMAdult (>18 years old)Female
Normal		 details
BloodDetected and Quantified0.577 +/- 0.322 uMAdult (>18 years old)Both
Normal		 details
BloodDetected and Quantified0.660 +/- 0.270 uMAdult (>18 years old)Male
Normal		 details
BloodDetected and Quantified0.266 +/- 0.127 uMAdult (>18 years old)Female
Normal		 details
Breast MilkDetected but not QuantifiedNot QuantifiedAdult (>18 years old)FemaleNormal details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified0.009 (0.008-0.01) uMAdult (>18 years old)FemaleEndometrial cancer details
BloodDetected and Quantified0.444 +/- 0.420 uMAdult (>18 years old)Not Specified
Obese		 details
BloodDetected and Quantified0.608 +/- 0.690 uMAdult (>18 years old)Not Specified
Overweight		 details
BloodDetected and Quantified0.560 +/- 0.290 uMAdult (>18 years old)BothType I diabetes details
BloodDetected and Quantified0.380 +/- 0.220 uMChildren (1 - 13 years old)Not SpecifiedObese details
BloodDetected and Quantified0.450 +/- 0.270 uMChildren (1 - 13 years old)Not SpecifiedOverweight details
Associated Disorders and Diseases
Disease References
Endometrial cancer
  1. Jeong NH, Song ES, Lee JM, Lee KB, Kim MK, Yun YM, Lee JK, Son SK, Lee JP, Kim JH, Hur SY, Kwon YI: Preoperative levels of plasma micronutrients are related to endometrial cancer risk. Acta Obstet Gynecol Scand. 2009;88(4):434-9. doi: 10.1080/00016340902767187. [PubMed:19235557 ]
Obesity
  1. Vioque J, Weinbrenner T, Asensio L, Castello A, Young IS, Fletcher A: Plasma concentrations of carotenoids and vitamin C are better correlated with dietary intake in normal weight than overweight and obese elderly subjects. Br J Nutr. 2007 May;97(5):977-86. [PubMed:17408529 ]
  2. Burrows TL, Warren JM, Colyvas K, Garg ML, Collins CE: Validation of overweight children's fruit and vegetable intake using plasma carotenoids. Obesity (Silver Spring). 2009 Jan;17(1):162-8. doi: 10.1038/oby.2008.495. Epub 2008 Nov 6. [PubMed:18997681 ]
Diabetes mellitus type 1
  1. Granado-Lorencio F, Olmedilla-Alonso B, Blanco-Navarro I, Botella-Romero F, Simal-Anton A: Assessment of carotenoid status and the relation to glycaemic control in type I diabetics: a follow-up study. Eur J Clin Nutr. 2006 Aug;60(8):1000-8. Epub 2006 Feb 1. [PubMed:16452910 ]
Associated OMIM IDs
DrugBank IDDB11231
Phenol Explorer Compound IDNot Available
FooDB IDFDB014534
KNApSAcK IDC00000911
Chemspider ID394156
KEGG Compound IDC05432
BioCyc IDCPD1F-114
BiGG IDNot Available
Wikipedia LinkLycopene
METLIN IDNot Available
PubChem Compound446925
PDB IDNot Available
ChEBI ID15948
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDMDB00000408
Good Scents IDrw1030761
References
Synthesis ReferenceIto, Shuichi; Yamaguchi, Yuzo. Fermentative production of lycopene. Jpn. Tokkyo Koho (1973), 5 pp.
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. Stahl W, Schwarz W, Sundquist AR, Sies H: cis-trans isomers of lycopene and beta-carotene in human serum and tissues. Arch Biochem Biophys. 1992 Apr;294(1):173-7. [PubMed:1550343 ]
  2. Aust O, Stahl W, Sies H, Tronnier H, Heinrich U: Supplementation with tomato-based products increases lycopene, phytofluene, and phytoene levels in human serum and protects against UV-light-induced erythema. Int J Vitam Nutr Res. 2005 Jan;75(1):54-60. [PubMed:15830922 ]
  3. Sengupta A, Das S: The anti-carcinogenic role of lycopene, abundantly present in tomato. Eur J Cancer Prev. 1999 Aug;8(4):325-30. [PubMed:10493308 ]
  4. Porrini M, Riso P: Lymphocyte lycopene concentration and DNA protection from oxidative damage is increased in women after a short period of tomato consumption. J Nutr. 2000 Feb;130(2):189-92. [PubMed:10720168 ]
  5. Bohm V, Bitsch R: Intestinal absorption of lycopene from different matrices and interactions to other carotenoids, the lipid status, and the antioxidant capacity of human plasma. Eur J Nutr. 1999 Jun;38(3):118-25. [PubMed:10443333 ]
  6. Stahl W, von Laar J, Martin HD, Emmerich T, Sies H: Stimulation of gap junctional communication: comparison of acyclo-retinoic acid and lycopene. Arch Biochem Biophys. 2000 Jan 1;373(1):271-4. [PubMed:10620348 ]
  7. Kravchenko LV, Morozov SV, Beketova NA, Deryagina VP, Avren'eva LI, Tutel'yan VA: Antioxidant status of rats receiving lycopene in different doses. Bull Exp Biol Med. 2003 Apr;135(4):353-7. [PubMed:12910307 ]
  8. Zaripheh S, Nara TY, Nakamura MT, Erdman JW Jr: Dietary lycopene downregulates carotenoid 15,15'-monooxygenase and PPAR-gamma in selected rat tissues. J Nutr. 2006 Apr;136(4):932-8. [PubMed:16549453 ]
  9. Hsiao G, Wang Y, Tzu NH, Fong TH, Shen MY, Lin KH, Chou DS, Sheu JR: Inhibitory effects of lycopene on in vitro platelet activation and in vivo prevention of thrombus formation. J Lab Clin Med. 2005 Oct;146(4):216-26. [PubMed:16194683 ]
  10. Gerster H: The potential role of lycopene for human health. J Am Coll Nutr. 1997 Apr;16(2):109-26. [PubMed:9100211 ]
  11. Stahl W, Sies H: Carotenoids and protection against solar UV radiation. Skin Pharmacol Appl Skin Physiol. 2002 Sep-Oct;15(5):291-6. [PubMed:12239422 ]
  12. Ermakov IV, Ermakova MR, Gellermann W, Lademann J: Noninvasive selective detection of lycopene and beta-carotene in human skin using Raman spectroscopy. J Biomed Opt. 2004 Mar-Apr;9(2):332-8. [PubMed:15065899 ]
  13. Walfisch Y, Walfisch S, Agbaria R, Levy J, Sharoni Y: Lycopene in serum, skin and adipose tissues after tomato-oleoresin supplementation in patients undergoing haemorrhoidectomy or peri-anal fistulotomy. Br J Nutr. 2003 Oct;90(4):759-66. [PubMed:13129444 ]
  14. Ribaya-Mercado JD, Garmyn M, Gilchrest BA, Russell RM: Skin lycopene is destroyed preferentially over beta-carotene during ultraviolet irradiation in humans. J Nutr. 1995 Jul;125(7):1854-9. [PubMed:7616301 ]
  15. Yeh S, Hu M: Antioxidant and pro-oxidant effects of lycopene in comparison with beta-carotene on oxidant-induced damage in Hs68 cells. J Nutr Biochem. 2000 Nov;11(11-12):548-554. [PubMed:11137891 ]
  16. Riso P, Visioli F, Erba D, Testolin G, Porrini M: Lycopene and vitamin C concentrations increase in plasma and lymphocytes after tomato intake. Effects on cellular antioxidant protection. Eur J Clin Nutr. 2004 Oct;58(10):1350-8. [PubMed:15054415 ]
  17. Arab L, Steck S: Lycopene and cardiovascular disease. Am J Clin Nutr. 2000 Jun;71(6 Suppl):1691S-5S; discussion 1696S-7S. [PubMed:10837319 ]
  18. Michael McClain R, Bausch J: Summary of safety studies conducted with synthetic lycopene. Regul Toxicol Pharmacol. 2003 Apr;37(2):274-85. [PubMed:12726756 ]

Enzymes

Enzyme Details
1. Beta,beta-carotene 9',10'-oxygenase
General function:
Secondary metabolites biosynthesis, transport and catabolism
Specific function:
Asymmetrically cleaves beta-carotene at the 9',10' double bond resulting in the formation of beta-apo-10'-carotenal and beta-ionone. Besides beta-carotene, lycopene is also oxidatively cleaved. The apocarotenals formed by this enzyme may be the precursors for the biosynthesis of retinoic acid or exert unknown physiological effects.
Gene Name:
BCO2
Uniprot ID:
Q9BYV7
Molecular weight:
61509.65