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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2006-05-22 14:17:46 UTC

Update Date

2022-03-07 02:49:14 UTC

HMDB ID

HMDB0002297

Secondary Accession Numbers

HMDB02297

Metabolite Identification

Common Name

5-cis-Lycopene

Description

5-cis-Lycopene is a carotenoid found in human fluids. Carotenoids are isoprenoid molecules that are widespread in nature and are typically seen as pigments in fruits, flowers, birds and crustacea. Animals are unable to synthesise carotenoids de novo, and rely upon the diet as a source of these compounds. Over recent years there has been considerable interest in dietary carotenoids with respect to their potential in alleviating age-related diseases in humans. This attention has been mirrored by significant advances in cloning most of the carotenoid genes and in the genetic manipulation of crop plants with the intention of increasing levels in the diet. Studies have shown an inverse relationship between the consumption of certain fruits and vegetables and the risk of epithelial cancer. Since carotenoids are among the micronutrients found in cancer preventive foods, detailed qualitative and quantitative determination of these compounds, particularly in fruits and vegetables and in human plasma, have recently become increasingly important (PMID: 15003396 ).

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI


  Mrv1652303202019492D          

 40 39  0  0  0  0            999 V2000
 9991.6782 9986.9015    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9990.9647 9987.3135    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9990.2491 9986.9015    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9989.5335 9987.3135    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9988.8200 9986.9015    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9988.1044 9987.3135    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9987.3888 9986.9015    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9986.6751 9987.3135    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9985.9602 9986.9015    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9985.2434 9987.3135    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9984.5286 9986.9015    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9983.8138 9987.3135    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9983.0990 9986.9015    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9982.3842 9987.3135    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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 9980.9546 9987.3135    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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 9975.9509 9986.9015    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9976.6658 9988.1384    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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 9991.6782 9986.0760    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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 9996.6751 9985.6623    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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 9997.3892 9986.0735    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 32  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
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 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
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 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
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 31 33  2  0  0  0  0
 33 34  1  0  0  0  0
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 34 36  1  0  0  0  0
 36 37  1  0  0  0  0
 37 38  2  0  0  0  0
 38 39  1  0  0  0  0
 38 40  1  0  0  0  0
M  END

HMDB0002297
     RDKit          3D
5-cis-Lycopene
 96 95  0  0  0  0  0  0  0  0999 V2000
  -10.2070    0.2294    1.0625 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.9203   -0.0546    0.2406 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -6.1142   -1.8014    1.1862 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9112   -2.0180    2.4404 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4588   -3.3239    2.7412 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0279   -0.9671    3.3033 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3926    0.2234    3.0220 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2154    1.5034    3.3439 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2491    2.1520    2.5290 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0234    1.1626    2.1784 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8378    3.3839    2.2397 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7958    3.4796    1.3025 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0798    4.4187    0.6641 C   0  0  0  0  0  0  0  0  0  0  0  0
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    9.5091   -1.3266    4.9660 C   0  0  0  0  0  0  0  0  0  0  0  0
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    9.1697   -2.2993    5.3117 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.5640   -1.2766    4.6816 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.2023   -0.5167    5.6962 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
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  6  7  1  0
  7  8  1  0
  7  9  2  0
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 39 93  1  0
 40 94  1  0
 40 95  1  0
 40 96  1  0
M  END


  Mrv1652303202019492D          

 40 39  0  0  0  0            999 V2000
 9991.6782 9986.9015    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9990.9647 9987.3135    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9990.2491 9986.9015    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9989.5335 9987.3135    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9988.8200 9986.9015    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9988.1044 9987.3135    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9987.3888 9986.9015    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9986.6751 9987.3135    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9985.9602 9986.9015    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9985.2434 9987.3135    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9984.5286 9986.9015    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9983.8138 9987.3135    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9983.0990 9986.9015    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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 9978.8102 9986.9015    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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 9976.6658 9987.3135    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9975.9509 9986.9015    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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  1  2  2  0  0  0  0
  1 29  1  0  0  0  0
  1 32  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
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 36 37  1  0  0  0  0
 37 38  2  0  0  0  0
 38 39  1  0  0  0  0
 38 40  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0002297

> <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-IKZLVQEUSA-N

> <FORMULA>
C40H56

> <MOLECULAR_WEIGHT>
536.888

> <EXACT_MASS>
536.438201803

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_ATOM_COUNT>
96

> <JCHEM_AVERAGE_POLARIZABILITY>
72.7636533323486

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(6Z,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>
197.8060000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
16

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.97e-04 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(6Z,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

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0002297
     RDKit          3D
5-cis-Lycopene
 96 95  0  0  0  0  0  0  0  0999 V2000
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 40 96  1  0
M  END

HEADER    PROTEIN                                 20-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-MAR-20         0                                  
HETATM    1  C   UNK     0    8651.1338642.216   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0    8649.8018642.985   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0    8648.4658642.216   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0    8647.1298642.985   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0    8645.7978642.216   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0    8644.4628642.985   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0    8643.1268642.216   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0    8641.7948642.985   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0    8640.4598642.216   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0    8639.1218642.985   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0    8637.7878642.216   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0    8636.4528642.985   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0    8635.1188642.216   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0    8633.7848642.985   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0    8632.4508642.216   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0    8631.1158642.985   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0    8629.7818642.216   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0    8628.4468642.985   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0    8627.1128642.216   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0    8625.7788642.985   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0    8624.4448642.216   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0    8623.1098642.985   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0    8621.7758642.216   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0    8623.1098644.525   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0    8628.4468644.525   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0    8633.7848644.525   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0    8639.1218644.525   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0    8645.7978640.675   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0    8652.4688642.985   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0    8653.8008642.216   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0    8655.1368642.985   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0    8651.1338640.675   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0    8656.4678642.215   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0    8656.4658640.677   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0    8657.8008642.982   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0    8657.7968639.906   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0    8659.1298640.674   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0    8660.4608639.903   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0    8660.4598638.365   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0    8661.7938640.671   0.000  0.00  0.00           C+0
CONECT    1    2   29   32                                                  
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   33                                                       
CONECT   32    1                                                            
CONECT   33   31   34   35                                                  
CONECT   34   33   36                                                       
CONECT   35   33                                                            
CONECT   36   34   37                                                       
CONECT   37   36   38                                                       
CONECT   38   37   39   40                                                  
CONECT   39   38                                                            
CONECT   40   38                                                            
MASTER        0    0    0    0    0    0    0    0   40    0   78    0
END

COMPND    HMDB0002297
HETATM    1  C1  UNL     1     -10.207   0.229   1.062  1.00  0.00           C  
HETATM    2  C2  UNL     1      -8.920  -0.055   0.241  1.00  0.00           C  
HETATM    3  C3  UNL     1      -8.456   1.032  -0.697  1.00  0.00           C  
HETATM    4  C4  UNL     1      -8.369  -1.166   0.484  1.00  0.00           C  
HETATM    5  C5  UNL     1      -7.186  -1.940   0.017  1.00  0.00           C  
HETATM    6  C6  UNL     1      -6.114  -1.801   1.186  1.00  0.00           C  
HETATM    7  C7  UNL     1      -6.911  -2.018   2.440  1.00  0.00           C  
HETATM    8  C8  UNL     1      -7.459  -3.324   2.741  1.00  0.00           C  
HETATM    9  C9  UNL     1      -7.028  -0.967   3.303  1.00  0.00           C  
HETATM   10  C10 UNL     1      -6.393   0.223   3.022  1.00  0.00           C  
HETATM   11  C11 UNL     1      -6.215   1.503   3.344  1.00  0.00           C  
HETATM   12  C12 UNL     1      -5.249   2.152   2.529  1.00  0.00           C  
HETATM   13  C13 UNL     1      -4.023   1.163   2.178  1.00  0.00           C  
HETATM   14  C14 UNL     1      -4.838   3.384   2.240  1.00  0.00           C  
HETATM   15  C15 UNL     1      -3.796   3.480   1.302  1.00  0.00           C  
HETATM   16  C16 UNL     1      -3.080   4.419   0.664  1.00  0.00           C  
HETATM   17  C17 UNL     1      -2.059   3.957  -0.213  1.00  0.00           C  
HETATM   18  C18 UNL     1      -1.558   2.551  -0.030  1.00  0.00           C  
HETATM   19  C19 UNL     1      -1.320   4.656  -1.133  1.00  0.00           C  
HETATM   20  C20 UNL     1      -0.423   3.805  -1.800  1.00  0.00           C  
HETATM   21  C21 UNL     1       0.437   3.867  -2.833  1.00  0.00           C  
HETATM   22  C22 UNL     1       1.149   2.668  -3.088  1.00  0.00           C  
HETATM   23  C23 UNL     1       1.922   2.150  -3.996  1.00  0.00           C  
HETATM   24  C24 UNL     1       2.142   3.046  -5.157  1.00  0.00           C  
HETATM   25  C25 UNL     1       2.674   0.961  -3.670  1.00  0.00           C  
HETATM   26  C26 UNL     1       3.329   0.120  -4.412  1.00  0.00           C  
HETATM   27  C27 UNL     1       4.023  -0.987  -3.863  1.00  0.00           C  
HETATM   28  C28 UNL     1       4.645  -2.012  -3.729  1.00  0.00           C  
HETATM   29  C29 UNL     1       4.590  -2.212  -5.580  1.00  0.00           C  
HETATM   30  C30 UNL     1       5.336  -3.168  -3.593  1.00  0.00           C  
HETATM   31  C31 UNL     1       6.139  -2.996  -2.501  1.00  0.00           C  
HETATM   32  C32 UNL     1       7.067  -3.187  -1.466  1.00  0.00           C  
HETATM   33  C33 UNL     1       7.423  -2.251  -0.638  1.00  0.00           C  
HETATM   34  C34 UNL     1       6.871  -0.887  -0.748  1.00  0.00           C  
HETATM   35  C35 UNL     1       8.350  -2.516   0.505  1.00  0.00           C  
HETATM   36  C36 UNL     1       7.571  -2.026   1.727  1.00  0.00           C  
HETATM   37  C37 UNL     1       8.451  -2.133   2.925  1.00  0.00           C  
HETATM   38  C38 UNL     1       8.637  -1.105   3.696  1.00  0.00           C  
HETATM   39  C39 UNL     1       8.110   0.243   3.594  1.00  0.00           C  
HETATM   40  C40 UNL     1       9.509  -1.327   4.966  1.00  0.00           C  
HETATM   41  H1  UNL     1     -10.957   0.259   0.286  1.00  0.00           H  
HETATM   42  H2  UNL     1     -10.347  -0.528   1.840  1.00  0.00           H  
HETATM   43  H3  UNL     1     -10.058   1.224   1.529  1.00  0.00           H  
HETATM   44  H4  UNL     1      -7.420   0.961  -0.947  1.00  0.00           H  
HETATM   45  H5  UNL     1      -9.158   1.028  -1.592  1.00  0.00           H  
HETATM   46  H6  UNL     1      -8.662   1.976  -0.164  1.00  0.00           H  
HETATM   47  H7  UNL     1      -8.929  -1.825   1.244  1.00  0.00           H  
HETATM   48  H8  UNL     1      -7.345  -2.970  -0.197  1.00  0.00           H  
HETATM   49  H9  UNL     1      -6.806  -1.386  -0.881  1.00  0.00           H  
HETATM   50  H10 UNL     1      -5.592  -0.930   0.983  1.00  0.00           H  
HETATM   51  H11 UNL     1      -5.434  -2.678   0.994  1.00  0.00           H  
HETATM   52  H12 UNL     1      -7.121  -3.652   3.774  1.00  0.00           H  
HETATM   53  H13 UNL     1      -8.542  -3.471   2.789  1.00  0.00           H  
HETATM   54  H14 UNL     1      -7.014  -4.102   2.030  1.00  0.00           H  
HETATM   55  H15 UNL     1      -7.621  -1.211   4.169  1.00  0.00           H  
HETATM   56  H16 UNL     1      -5.762   0.126   2.016  1.00  0.00           H  
HETATM   57  H17 UNL     1      -6.862   1.787   4.158  1.00  0.00           H  
HETATM   58  H18 UNL     1      -4.113   0.891   1.151  1.00  0.00           H  
HETATM   59  H19 UNL     1      -4.124   0.275   2.855  1.00  0.00           H  
HETATM   60  H20 UNL     1      -3.148   1.657   2.497  1.00  0.00           H  
HETATM   61  H21 UNL     1      -5.356   4.169   2.742  1.00  0.00           H  
HETATM   62  H22 UNL     1      -3.532   2.492   0.739  1.00  0.00           H  
HETATM   63  H23 UNL     1      -3.406   5.401   0.925  1.00  0.00           H  
HETATM   64  H24 UNL     1      -1.971   2.043   0.824  1.00  0.00           H  
HETATM   65  H25 UNL     1      -1.745   1.938  -0.898  1.00  0.00           H  
HETATM   66  H26 UNL     1      -0.446   2.586   0.168  1.00  0.00           H  
HETATM   67  H27 UNL     1      -1.530   5.686  -1.134  1.00  0.00           H  
HETATM   68  H28 UNL     1      -0.334   2.716  -1.453  1.00  0.00           H  
HETATM   69  H29 UNL     1       0.429   4.806  -3.301  1.00  0.00           H  
HETATM   70  H30 UNL     1       1.007   1.851  -2.250  1.00  0.00           H  
HETATM   71  H31 UNL     1       2.342   2.397  -6.055  1.00  0.00           H  
HETATM   72  H32 UNL     1       3.028   3.673  -5.004  1.00  0.00           H  
HETATM   73  H33 UNL     1       1.270   3.674  -5.368  1.00  0.00           H  
HETATM   74  H34 UNL     1       2.698   0.669  -2.551  1.00  0.00           H  
HETATM   75  H35 UNL     1       3.308   0.357  -5.502  1.00  0.00           H  
HETATM   76  H36 UNL     1       4.005  -0.755  -2.551  1.00  0.00           H  
HETATM   77  H37 UNL     1       5.619  -2.550  -5.595  1.00  0.00           H  
HETATM   78  H38 UNL     1       4.442  -1.227  -5.854  1.00  0.00           H  
HETATM   79  H39 UNL     1       3.795  -2.943  -5.508  1.00  0.00           H  
HETATM   80  H40 UNL     1       5.623  -4.159  -3.732  1.00  0.00           H  
HETATM   81  H41 UNL     1       5.633  -1.898  -2.187  1.00  0.00           H  
HETATM   82  H42 UNL     1       7.530  -4.215  -1.334  1.00  0.00           H  
HETATM   83  H43 UNL     1       6.900  -0.611  -1.876  1.00  0.00           H  
HETATM   84  H44 UNL     1       7.566  -0.152  -0.275  1.00  0.00           H  
HETATM   85  H45 UNL     1       5.882  -0.736  -0.333  1.00  0.00           H  
HETATM   86  H46 UNL     1       8.574  -3.583   0.576  1.00  0.00           H  
HETATM   87  H47 UNL     1       9.282  -1.915   0.384  1.00  0.00           H  
HETATM   88  H48 UNL     1       6.612  -2.618   1.843  1.00  0.00           H  
HETATM   89  H49 UNL     1       7.268  -0.985   1.571  1.00  0.00           H  
HETATM   90  H50 UNL     1       8.925  -3.099   3.150  1.00  0.00           H  
HETATM   91  H51 UNL     1       7.137   0.426   4.102  1.00  0.00           H  
HETATM   92  H52 UNL     1       7.926   0.522   2.514  1.00  0.00           H  
HETATM   93  H53 UNL     1       8.825   1.040   3.979  1.00  0.00           H  
HETATM   94  H54 UNL     1       9.170  -2.299   5.312  1.00  0.00           H  
HETATM   95  H55 UNL     1      10.564  -1.277   4.682  1.00  0.00           H  
HETATM   96  H56 UNL     1       9.202  -0.517   5.696  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

HMDB0002297
     RDKit          3D
5-cis-Lycopene
 96 95  0  0  0  0  0  0  0  0999 V2000
  -10.2070    0.2294    1.0625 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.9203   -0.0546    0.2406 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.4557    1.0320   -0.6972 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.3691   -1.1656    0.4842 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1862   -1.9403    0.0168 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1142   -1.8014    1.1862 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9112   -2.0180    2.4404 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4588   -3.3239    2.7412 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0279   -0.9671    3.3033 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3926    0.2234    3.0220 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2154    1.5034    3.3439 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2491    2.1520    2.5290 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0234    1.1626    2.1784 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8378    3.3839    2.2397 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7958    3.4796    1.3025 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0798    4.4187    0.6641 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0588    3.9569   -0.2131 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5584    2.5514   -0.0296 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3203    4.6556   -1.1327 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4233    3.8052   -1.7997 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4375    3.8670   -2.8327 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1490    2.6676   -3.0884 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9222    2.1499   -3.9964 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1419    3.0461   -5.1567 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6742    0.9615   -3.6700 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3293    0.1204   -4.4124 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0229   -0.9868   -3.8626 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6448   -2.0125   -3.7295 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5899   -2.2122   -5.5799 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3362   -3.1678   -3.5929 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1387   -2.9960   -2.5013 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0671   -3.1872   -1.4659 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4230   -2.2507   -0.6378 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8714   -0.8869   -0.7477 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.3499   -2.5158    0.5052 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.5710   -2.0264    1.7273 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.4515   -2.1332    2.9252 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.6365   -1.1046    3.6962 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.1099    0.2431    3.5943 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.5091   -1.3266    4.9660 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.9572    0.2589    0.2860 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.3470   -0.5279    1.8402 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.0576    1.2240    1.5294 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4200    0.9613   -0.9471 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.1577    1.0276   -1.5920 H   0  0  0  0  0  0  0  0  0  0  0  0
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    3.7953   -2.9433   -5.5079 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6234   -4.1594   -3.7319 H   0  0  0  0  0  0  0  0  0  0  0  0
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    7.2682   -0.9854    1.5713 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.9254   -3.0993    3.1504 H   0  0  0  0  0  0  0  0  0  0  0  0
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    9.2023   -0.5167    5.6962 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
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M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
(5Z)-Lycopene	HMDB
5-cis-Psi,psi-carotene	HMDB
5-cis-Ψ,ψ-carotene	HMDB
5-cis-Lycopene	HMDB

Chemical Formula

C₄₀H₅₆

Average Molecular Weight

536.888

Monoisotopic Molecular Weight

536.438201803

IUPAC Name

(6Z,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 Name

(6Z,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

CAS Registry Number

101468-86-4

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-IKZLVQEUSA-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.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Tetraterpenoids

Direct Parent

Carotenes

Alternative Parents

Substituents

Carotene
Branched unsaturated hydrocarbon
Unsaturated aliphatic hydrocarbon
Unsaturated hydrocarbon
Olefin
Acyclic olefin
Hydrocarbon
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 21902859)

Cellular substructure

Extracellular (HMDB: HMDB0002297)
Membrane (HMDB: HMDB0002297)

Process

Not Available

Role

Not Available

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	0.0004 g/L	ALOGPS
logP	9.16	ALOGPS
logP	11.93	ChemAxon
logS	-6.1	ALOGPS
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	0	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	0 Å²	ChemAxon
Rotatable Bond Count	16	ChemAxon
Refractivity	197.81 m³·mol⁻¹	ChemAxon
Polarizability	72.76 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DeepCCS	[M+H]+	251.16	30932474
DeepCCS	[M-H]-	249.264	30932474
DeepCCS	[M-2H]-	282.504	30932474
DeepCCS	[M+Na]+	256.868	30932474
AllCCS	[M+H]+	237.0	32859911
AllCCS	[M+H-H2O]+	235.4	32859911
AllCCS	[M+NH4]+	238.6	32859911
AllCCS	[M+Na]+	239.0	32859911
AllCCS	[M-H]-	228.3	32859911
AllCCS	[M+Na-2H]-	230.2	32859911
AllCCS	[M+HCOO]-	232.4	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
5-cis-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	5089.1	Standard polar	33892256
5-cis-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	4285.6	Standard non polar	33892256
5-cis-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	3938.3	Semi standard non polar	33892256

Spectra

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-cis-Lycopene 10V, Negative-QTOF	splash10-000i-0100090000-4ab68b33d589aeb3b2dd	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-cis-Lycopene 20V, Negative-QTOF	splash10-000i-0926580000-889c9c655f28c8c703c8	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-cis-Lycopene 40V, Negative-QTOF	splash10-0gb9-0503910000-a80f0ec28aa2775d93e0	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-cis-Lycopene 10V, Positive-QTOF	splash10-000i-2235970000-73fc43e90358e2cae371	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-cis-Lycopene 20V, Positive-QTOF	splash10-0fc1-2011900000-667641d02a3eee5d267d	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-cis-Lycopene 40V, Positive-QTOF	splash10-0wb9-1223900000-52a07bb8af9e23809e6e	2021-09-24	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Extracellular
Membrane

Biospecimen Locations

Blood

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Male	Normal	21902859	details

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

9931680

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

11756979

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Fraser PD, Bramley PM: The biosynthesis and nutritional uses of carotenoids. Prog Lipid Res. 2004 May;43(3):228-65. [PubMed:15003396 ]

Showing metabocard for 5-cis-Lycopene (HMDB0002297)

MOL for HMDB0002297 (5-cis-Lycopene)

3D MOL for HMDB0002297 (5-cis-Lycopene)

3D SDF for HMDB0002297 (5-cis-Lycopene)

3D-SDF for HMDB0002297 (5-cis-Lycopene)

PDB for HMDB0002297 (5-cis-Lycopene)

3D PDB for HMDB0002297 (5-cis-Lycopene)

SMILES for HMDB0002297 (5-cis-Lycopene)

INCHI for HMDB0002297 (5-cis-Lycopene)

Structure for HMDB0002297 (5-cis-Lycopene)

3D Structure for HMDB0002297 (5-cis-Lycopene)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

MS/MS Spectra