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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2007-05-22 17:57:51 UTC

Update Date

2022-03-07 02:49:30 UTC

HMDB ID

HMDB0006220

Secondary Accession Numbers

HMDB06220

Metabolite Identification

Common Name

13-cis-Retinal

Description

13-cis-Retinal is a naturally occurring retinoid. Retinoids are vitamin A analogs that have profound biological activities. Several retinoids have been reported to have antiinflammatory activity in certain animal models of arthritis, such as adjuvant-induced and streptococcal cell wall-induced arthritis in rats. Some retinoids also have been shown to possess antiinftammatory activity in man by their ability to modulate inflammatory diseases of the skin. It has been reported, for example, that retinoid treatment can inhibit neutrophil accumulation in cutaneous disorders such as psoriasis. (PMID:2123476 ).

Structure

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

HMDB0006220
     RDKit          3D
13-cis-Retinal
 49 49  0  0  0  0  0  0  0  0999 V2000
   -3.2054    1.7080   -1.6548 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5958    0.5315   -0.8302 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6014   -0.1460   -0.2110 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2719    0.3430   -0.4124 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1346   -0.0945    0.0672 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1705    0.5339   -0.2466 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1531    1.6922   -1.1346 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2609    0.0499    0.2622 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5660    0.6177   -0.0054 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6746    0.0995    0.5316 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9641    0.6980    0.2387 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0094    1.8975   -0.6711 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0918    0.2193    0.7478 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1018   -0.9238    1.6221 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.2345   -1.3069    2.0591 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0556   -1.3002    0.5738 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7776   -0.8245    1.8219 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0556   -2.3274    0.9787 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1121   -2.0302   -0.2910 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3516   -1.1460   -0.2413 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0212    0.2261   -0.7444 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1110    2.1668   -2.0793 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7284    2.5020   -1.0206 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5566    1.4378   -2.5159 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1334    1.2278   -1.0693 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1274   -0.9291    0.7260 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1061    2.1514   -1.3888 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6322    1.3808   -2.0772 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5512    2.4835   -0.6213 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2241   -0.8164    0.9195 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7171    1.4729   -0.6392 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5312   -0.7547    1.1656 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4681    2.7515   -0.2240 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5057    1.5736   -1.6131 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.0580    2.1539   -0.8530 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.0064    0.7537    0.4559 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2150   -1.4368    1.9006 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4158   -1.6282    2.2062 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9983   -0.5734    2.5914 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3354    0.1034    1.6357 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7009   -3.2592    1.2211 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4044   -2.7096    0.1913 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5965   -2.1196    1.9562 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7473   -2.0432   -1.3189 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3463   -3.0138    0.1024 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7881   -1.1457    0.7786 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0983   -1.6194   -0.9096 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4420    0.3303   -1.7935 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5293    1.0426   -0.1870 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  1  0
  6  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  1  0
 11 13  2  0
 13 14  1  0
 14 15  2  0
  3 16  1  0
 16 17  1  0
 16 18  1  0
 16 19  1  0
 19 20  1  0
 20 21  1  0
 21  2  1  0
  1 22  1  0
  1 23  1  0
  1 24  1  0
  4 25  1  0
  5 26  1  0
  7 27  1  0
  7 28  1  0
  7 29  1  0
  8 30  1  0
  9 31  1  0
 10 32  1  0
 12 33  1  0
 12 34  1  0
 12 35  1  0
 13 36  1  0
 14 37  1  0
 17 38  1  0
 17 39  1  0
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 18 41  1  0
 18 42  1  0
 18 43  1  0
 19 44  1  0
 19 45  1  0
 20 46  1  0
 20 47  1  0
 21 48  1  0
 21 49  1  0
M  END

  Mrv1652307301919572D          

 21 21  0  0  0  0            999 V2000
    2.8579    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1842    1.8695    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2448    1.8695    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3532    1.2202    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0868    0.7324    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  8  6  1  0  0  0  0
  9  6  2  0  0  0  0
 10  7  1  0  0  0  0
 12 11  2  0  0  0  0
 14  7  1  0  0  0  0
 15 13  1  0  0  0  0
 16  1  1  0  0  0  0
 16  8  2  0  0  0  0
 16 11  1  0  0  0  0
 17  2  1  0  0  0  0
 17  9  1  0  0  0  0
 17 13  2  0  0  0  0
 18  3  1  0  0  0  0
 18 10  1  0  0  0  0
 19 12  1  0  0  0  0
 19 18  2  0  0  0  0
 20  4  1  0  0  0  0
 20  5  1  0  0  0  0
 20 14  1  0  0  0  0
 20 19  1  0  0  0  0
 21 15  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0006220

> <DATABASE_NAME>
hmdb

> <SMILES>
C\C(\C=C\C=C(/C)\C=C\C1=C(C)CCCC1(C)C)=C\C=O

> <INCHI_IDENTIFIER>
InChI=1S/C20H28O/c1-16(8-6-9-17(2)13-15-21)11-12-19-18(3)10-7-14-20(19,4)5/h6,8-9,11-13,15H,7,10,14H2,1-5H3/b9-6+,12-11+,16-8+,17-13-

> <INCHI_KEY>
NCYCYZXNIZJOKI-HWCYFHEPSA-N

> <FORMULA>
C20H28O

> <MOLECULAR_WEIGHT>
284.4357

> <EXACT_MASS>
284.214015518

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
49

> <JCHEM_AVERAGE_POLARIZABILITY>
35.469533558432445

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2Z,4E,6E,8E)-3,7-dimethyl-9-(2,6,6-trimethylcyclohex-1-en-1-yl)nona-2,4,6,8-tetraenal

> <JCHEM_LOGP>
4.855751458666667

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-4.061304726121949

> <JCHEM_POLAR_SURFACE_AREA>
17.07

> <JCHEM_REFRACTIVITY>
96.86540000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
13-cis retinal

> <JCHEM_VEBER_RULE>
1

$$$$

HMDB0006220
     RDKit          3D
13-cis-Retinal
 49 49  0  0  0  0  0  0  0  0999 V2000
   -3.2054    1.7080   -1.6548 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5958    0.5315   -0.8302 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6014   -0.1460   -0.2110 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2719    0.3430   -0.4124 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1346   -0.0945    0.0672 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1705    0.5339   -0.2466 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1531    1.6922   -1.1346 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2609    0.0499    0.2622 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5660    0.6177   -0.0054 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6746    0.0995    0.5316 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9641    0.6980    0.2387 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0094    1.8975   -0.6711 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0918    0.2193    0.7478 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1018   -0.9238    1.6221 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.2345   -1.3069    2.0591 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0556   -1.3002    0.5738 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7776   -0.8245    1.8219 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0556   -2.3274    0.9787 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1121   -2.0302   -0.2910 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3516   -1.1460   -0.2413 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0212    0.2261   -0.7444 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1110    2.1668   -2.0793 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7284    2.5020   -1.0206 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5566    1.4378   -2.5159 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1334    1.2278   -1.0693 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1274   -0.9291    0.7260 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1061    2.1514   -1.3888 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6322    1.3808   -2.0772 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5512    2.4835   -0.6213 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2241   -0.8164    0.9195 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7171    1.4729   -0.6392 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5312   -0.7547    1.1656 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4681    2.7515   -0.2240 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5057    1.5736   -1.6131 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.0580    2.1539   -0.8530 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.0064    0.7537    0.4559 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2150   -1.4368    1.9006 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4158   -1.6282    2.2062 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9983   -0.5734    2.5914 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3354    0.1034    1.6357 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7009   -3.2592    1.2211 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4044   -2.7096    0.1913 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5965   -2.1196    1.9562 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7473   -2.0432   -1.3189 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3463   -3.0138    0.1024 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7881   -1.1457    0.7786 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0983   -1.6194   -0.9096 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4420    0.3303   -1.7935 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5293    1.0426   -0.1870 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  1  0
  6  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  1  0
 11 13  2  0
 13 14  1  0
 14 15  2  0
  3 16  1  0
 16 17  1  0
 16 18  1  0
 16 19  1  0
 19 20  1  0
 20 21  1  0
 21  2  1  0
  1 22  1  0
  1 23  1  0
  1 24  1  0
  4 25  1  0
  5 26  1  0
  7 27  1  0
  7 28  1  0
  7 29  1  0
  8 30  1  0
  9 31  1  0
 10 32  1  0
 12 33  1  0
 12 34  1  0
 12 35  1  0
 13 36  1  0
 14 37  1  0
 17 38  1  0
 17 39  1  0
 17 40  1  0
 18 41  1  0
 18 42  1  0
 18 43  1  0
 19 44  1  0
 19 45  1  0
 20 46  1  0
 20 47  1  0
 21 48  1  0
 21 49  1  0
M  END

HEADER    PROTEIN                                 30-JUL-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   30-JUL-19         0                                  
HETATM    1  C   UNK     0       5.335   6.160   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      10.669   6.160   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.344   3.490   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.324   3.490   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       8.002   4.620   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.668   3.850   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       9.336   3.850   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.001   3.850   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      12.003   3.850   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      11.859   2.278   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.335   4.620   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      10.669   4.620   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      13.229   1.367   0.000  0.00  0.00           O+0
CONECT    1   16                                                            
CONECT    2   17                                                            
CONECT    3   18                                                            
CONECT    4   20                                                            
CONECT    5   20                                                            
CONECT    6    8    9                                                       
CONECT    7   10   14                                                       
CONECT    8    6   16                                                       
CONECT    9    6   17                                                       
CONECT   10    7   18                                                       
CONECT   11   12   16                                                       
CONECT   12   11   19                                                       
CONECT   13   15   17                                                       
CONECT   14    7   20                                                       
CONECT   15   13   21                                                       
CONECT   16    1    8   11                                                  
CONECT   17    2    9   13                                                  
CONECT   18    3   10   19                                                  
CONECT   19   12   18   20                                                  
CONECT   20    4    5   14   19                                             
CONECT   21   15                                                            
MASTER        0    0    0    0    0    0    0    0   21    0   42    0
END

COMPND    HMDB0006220
HETATM    1  C1  UNL     1      -3.205   1.708  -1.655  1.00  0.00           C  
HETATM    2  C2  UNL     1      -3.596   0.531  -0.830  1.00  0.00           C  
HETATM    3  C3  UNL     1      -2.601  -0.146  -0.211  1.00  0.00           C  
HETATM    4  C4  UNL     1      -1.272   0.343  -0.412  1.00  0.00           C  
HETATM    5  C5  UNL     1      -0.135  -0.095   0.067  1.00  0.00           C  
HETATM    6  C6  UNL     1       1.171   0.534  -0.247  1.00  0.00           C  
HETATM    7  C7  UNL     1       1.153   1.692  -1.135  1.00  0.00           C  
HETATM    8  C8  UNL     1       2.261   0.050   0.262  1.00  0.00           C  
HETATM    9  C9  UNL     1       3.566   0.618  -0.005  1.00  0.00           C  
HETATM   10  C10 UNL     1       4.675   0.100   0.532  1.00  0.00           C  
HETATM   11  C11 UNL     1       5.964   0.698   0.239  1.00  0.00           C  
HETATM   12  C12 UNL     1       6.009   1.898  -0.671  1.00  0.00           C  
HETATM   13  C13 UNL     1       7.092   0.219   0.748  1.00  0.00           C  
HETATM   14  C14 UNL     1       7.102  -0.924   1.622  1.00  0.00           C  
HETATM   15  O1  UNL     1       8.234  -1.307   2.059  1.00  0.00           O  
HETATM   16  C15 UNL     1      -3.056  -1.300   0.574  1.00  0.00           C  
HETATM   17  C16 UNL     1      -3.778  -0.825   1.822  1.00  0.00           C  
HETATM   18  C17 UNL     1      -2.056  -2.327   0.979  1.00  0.00           C  
HETATM   19  C18 UNL     1      -4.112  -2.030  -0.291  1.00  0.00           C  
HETATM   20  C19 UNL     1      -5.352  -1.146  -0.241  1.00  0.00           C  
HETATM   21  C20 UNL     1      -5.021   0.226  -0.744  1.00  0.00           C  
HETATM   22  H1  UNL     1      -4.111   2.167  -2.079  1.00  0.00           H  
HETATM   23  H2  UNL     1      -2.728   2.502  -1.021  1.00  0.00           H  
HETATM   24  H3  UNL     1      -2.557   1.438  -2.516  1.00  0.00           H  
HETATM   25  H4  UNL     1      -1.133   1.228  -1.069  1.00  0.00           H  
HETATM   26  H5  UNL     1      -0.127  -0.929   0.726  1.00  0.00           H  
HETATM   27  H6  UNL     1       2.106   2.151  -1.389  1.00  0.00           H  
HETATM   28  H7  UNL     1       0.632   1.381  -2.077  1.00  0.00           H  
HETATM   29  H8  UNL     1       0.551   2.483  -0.621  1.00  0.00           H  
HETATM   30  H9  UNL     1       2.224  -0.816   0.920  1.00  0.00           H  
HETATM   31  H10 UNL     1       3.717   1.473  -0.639  1.00  0.00           H  
HETATM   32  H11 UNL     1       4.531  -0.755   1.166  1.00  0.00           H  
HETATM   33  H12 UNL     1       5.468   2.751  -0.224  1.00  0.00           H  
HETATM   34  H13 UNL     1       5.506   1.574  -1.613  1.00  0.00           H  
HETATM   35  H14 UNL     1       7.058   2.154  -0.853  1.00  0.00           H  
HETATM   36  H15 UNL     1       8.006   0.754   0.456  1.00  0.00           H  
HETATM   37  H16 UNL     1       6.215  -1.437   1.901  1.00  0.00           H  
HETATM   38  H17 UNL     1      -4.416  -1.628   2.206  1.00  0.00           H  
HETATM   39  H18 UNL     1      -2.998  -0.573   2.591  1.00  0.00           H  
HETATM   40  H19 UNL     1      -4.335   0.103   1.636  1.00  0.00           H  
HETATM   41  H20 UNL     1      -2.701  -3.259   1.221  1.00  0.00           H  
HETATM   42  H21 UNL     1      -1.404  -2.710   0.191  1.00  0.00           H  
HETATM   43  H22 UNL     1      -1.596  -2.120   1.956  1.00  0.00           H  
HETATM   44  H23 UNL     1      -3.747  -2.043  -1.319  1.00  0.00           H  
HETATM   45  H24 UNL     1      -4.346  -3.014   0.102  1.00  0.00           H  
HETATM   46  H25 UNL     1      -5.788  -1.146   0.779  1.00  0.00           H  
HETATM   47  H26 UNL     1      -6.098  -1.619  -0.910  1.00  0.00           H  
HETATM   48  H27 UNL     1      -5.442   0.330  -1.793  1.00  0.00           H  
HETATM   49  H28 UNL     1      -5.529   1.043  -0.187  1.00  0.00           H  
CONECT    1    2   22   23   24
CONECT    2    3    3   21
CONECT    3    4   16
CONECT    4    5    5   25
CONECT    5    6   26
CONECT    6    7    8    8
CONECT    7   27   28   29
CONECT    8    9   30
CONECT    9   10   10   31
CONECT   10   11   32
CONECT   11   12   13   13
CONECT   12   33   34   35
CONECT   13   14   36
CONECT   14   15   15   37
CONECT   16   17   18   19
CONECT   17   38   39   40
CONECT   18   41   42   43
CONECT   19   20   44   45
CONECT   20   21   46   47
CONECT   21   48   49
END

HMDB0006220
     RDKit          3D
13-cis-Retinal
 49 49  0  0  0  0  0  0  0  0999 V2000
   -3.2054    1.7080   -1.6548 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5958    0.5315   -0.8302 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6014   -0.1460   -0.2110 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2719    0.3430   -0.4124 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1346   -0.0945    0.0672 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1705    0.5339   -0.2466 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1531    1.6922   -1.1346 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2609    0.0499    0.2622 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5660    0.6177   -0.0054 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6746    0.0995    0.5316 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9641    0.6980    0.2387 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0094    1.8975   -0.6711 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0918    0.2193    0.7478 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1018   -0.9238    1.6221 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.2345   -1.3069    2.0591 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0556   -1.3002    0.5738 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7776   -0.8245    1.8219 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0556   -2.3274    0.9787 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1121   -2.0302   -0.2910 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3516   -1.1460   -0.2413 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0212    0.2261   -0.7444 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1110    2.1668   -2.0793 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7284    2.5020   -1.0206 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5566    1.4378   -2.5159 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1334    1.2278   -1.0693 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1274   -0.9291    0.7260 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1061    2.1514   -1.3888 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6322    1.3808   -2.0772 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5512    2.4835   -0.6213 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2241   -0.8164    0.9195 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7171    1.4729   -0.6392 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5312   -0.7547    1.1656 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4681    2.7515   -0.2240 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5057    1.5736   -1.6131 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.0580    2.1539   -0.8530 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.0064    0.7537    0.4559 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2150   -1.4368    1.9006 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4158   -1.6282    2.2062 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9983   -0.5734    2.5914 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3354    0.1034    1.6357 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7009   -3.2592    1.2211 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4044   -2.7096    0.1913 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5965   -2.1196    1.9562 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7473   -2.0432   -1.3189 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3463   -3.0138    0.1024 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7881   -1.1457    0.7786 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0983   -1.6194   -0.9096 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4420    0.3303   -1.7935 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5293    1.0426   -0.1870 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  1  0
  6  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  1  0
 11 13  2  0
 13 14  1  0
 14 15  2  0
  3 16  1  0
 16 17  1  0
 16 18  1  0
 16 19  1  0
 19 20  1  0
 20 21  1  0
 21  2  1  0
  1 22  1  0
  1 23  1  0
  1 24  1  0
  4 25  1  0
  5 26  1  0
  7 27  1  0
  7 28  1  0
  7 29  1  0
  8 30  1  0
  9 31  1  0
 10 32  1  0
 12 33  1  0
 12 34  1  0
 12 35  1  0
 13 36  1  0
 14 37  1  0
 17 38  1  0
 17 39  1  0
 17 40  1  0
 18 41  1  0
 18 42  1  0
 18 43  1  0
 19 44  1  0
 19 45  1  0
 20 46  1  0
 20 47  1  0
 21 48  1  0
 21 49  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
(13cis)-Retinal	ChEBI
(2Z,4E,6E,8E)-3,7-Dimethyl-9-(2,6,6-trimethylcyclohex-1-en-1-yl)nona-2,4,6,8-tetraenal	ChEBI
13-cis-Retinaldehyde	ChEBI
RETINAL	ChEBI
13Z-Retinal	HMDB
cis-13-Retinal	HMDB
Neoretinene a	HMDB
Neovitamin a aldehyde	HMDB
13-cis-Retinal	MeSH, HMDB

Chemical Formula

C₂₀H₂₈O

Average Molecular Weight

284.4357

Monoisotopic Molecular Weight

284.214015518

IUPAC Name

(2Z,4E,6E,8E)-3,7-dimethyl-9-(2,6,6-trimethylcyclohex-1-en-1-yl)nona-2,4,6,8-tetraenal

Traditional Name

13-cis retinal

CAS Registry Number

472-86-6

SMILES

C\C(\C=C\C=C(/C)\C=C\C1=C(C)CCCC1(C)C)=C\C=O

InChI Identifier

InChI=1S/C20H28O/c1-16(8-6-9-17(2)13-15-21)11-12-19-18(3)10-7-14-20(19,4)5/h6,8-9,11-13,15H,7,10,14H2,1-5H3/b9-6+,12-11+,16-8+,17-13-

InChI Key

NCYCYZXNIZJOKI-HWCYFHEPSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as retinoids. These are oxygenated derivatives of 3,7-dimethyl-1-(2,6,6-trimethylcyclohex-1-enyl)nona-1,3,5,7-tetraene and derivatives thereof.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Retinoids

Direct Parent

Retinoids

Alternative Parents

Substituents

Retinoid skeleton
Diterpenoid
Enal
Alpha,beta-unsaturated aldehyde
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Aldehyde
Aliphatic homomonocyclic compound

Molecular Framework

Aliphatic homomonocyclic compounds

External Descriptors

retinal (CHEBI:45487 )
Retinoids (LMPR01090018 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Source

Exogenous

Exogenous (HMDB: HMDB0006220)

Food

Animal origin

Poultry

Pheasant (FooDB: FOOD00430)
Squab (FooDB: FOOD00481)
Turkey (FooDB: FOOD00494)
Quail (FooDB: FOOD00541)
Anatidae (FooDB: FOOD00576)
Rock ptarmigan (FooDB: FOOD00597)
Columbidae (Dove, Pigeon) (FooDB: FOOD00610)
Chicken (FooDB: FOOD00329)
Mallard duck (FooDB: FOOD00353)
Emu (FooDB: FOOD00360)
Greylag goose (FooDB: FOOD00368)
Guinea hen (FooDB: FOOD00373)
Ostrich (FooDB: FOOD00422)
Velvet duck (FooDB: FOOD00427)

Lagomorph

Ovis

Sheep (Mutton, Lamb) (FooDB: FOOD00473)

Bovine

Venison

Deer (FooDB: FOOD00524)
Mule deer (FooDB: FOOD00348)
Elk (FooDB: FOOD00359)

Caprae

Domestic goat (FooDB: FOOD00529)

Swine

Domestic pig (FooDB: FOOD00536)
Wild boar (FooDB: FOOD00307)

Equine

Horse (FooDB: FOOD00378)

Endogenous

Endogenous (HMDB: HMDB0006220)

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	0.0042 g/L	ALOGPS
logP	4.86	ChemAxon
pKa (Strongest Basic)	-4.1	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	1	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	17.07 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	96.87 m³·mol⁻¹	ChemAxon
Polarizability	35.47 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	174.624	31661259
DarkChem	[M-H]-	174.959	31661259
DeepCCS	[M+H]+	189.365	30932474
DeepCCS	[M-H]-	187.007	30932474
DeepCCS	[M-2H]-	220.783	30932474
DeepCCS	[M+Na]+	196.009	30932474
AllCCS	[M+H]+	174.0	32859911
AllCCS	[M+H-H2O]+	170.7	32859911
AllCCS	[M+NH4]+	177.1	32859911
AllCCS	[M+Na]+	177.9	32859911
AllCCS	[M-H]-	178.3	32859911
AllCCS	[M+Na-2H]-	178.9	32859911
AllCCS	[M+HCOO]-	179.7	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
13-cis-Retinal	C\C(\C=C\C=C(/C)\C=C\C1=C(C)CCCC1(C)C)=C\C=O	3063.2	Standard polar	33892256
13-cis-Retinal	C\C(\C=C\C=C(/C)\C=C\C1=C(C)CCCC1(C)C)=C\C=O	2469.4	Standard non polar	33892256
13-cis-Retinal	C\C(\C=C\C=C(/C)\C=C\C1=C(C)CCCC1(C)C)=C\C=O	2398.5	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - 13-cis-Retinal GC-MS (Non-derivatized) - 70eV, Positive	splash10-014i-2290000000-df9d2aa7545cc60a54f9	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 13-cis-Retinal GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 13-cis-Retinal GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 13-cis-Retinal 10V, Positive-QTOF	splash10-000i-0490000000-f543f08fbaf94a2e3f8e	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 13-cis-Retinal 20V, Positive-QTOF	splash10-000i-3940000000-83ca23fc3e32f84b7d9b	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 13-cis-Retinal 40V, Positive-QTOF	splash10-0fri-9720000000-b077361f8a6c0a0a6c99	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 13-cis-Retinal 10V, Negative-QTOF	splash10-001i-0090000000-bad35938b77f181c29b9	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 13-cis-Retinal 20V, Negative-QTOF	splash10-001i-0090000000-1aadad0770df07f98436	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 13-cis-Retinal 40V, Negative-QTOF	splash10-00ko-4690000000-f624d342f88456375b9c	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 13-cis-Retinal 10V, Negative-QTOF	splash10-0a59-0090000000-2ec2f8f314943441fa15	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 13-cis-Retinal 20V, Negative-QTOF	splash10-0pb9-0190000000-312cebb17ccd0189ab4d	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 13-cis-Retinal 40V, Negative-QTOF	splash10-000i-1590000000-b2551eac481c0c930a4d	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 13-cis-Retinal 10V, Positive-QTOF	splash10-00n3-1960000000-43f8c66f164764c37361	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 13-cis-Retinal 20V, Positive-QTOF	splash10-0609-3920000000-dbeab0a82b306761cf6a	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 13-cis-Retinal 40V, Positive-QTOF	splash10-052f-7900000000-d2bb7c1aeeb87d8833d2	2021-09-22	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Experimental 2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, CDCl₃, experimental)	2018-05-25	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm
Extracellular
Membrane

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

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

FDB023844

KNApSAcK ID

Not Available

Chemspider ID

4940755

KEGG Compound ID

Not Available

BioCyc ID

CPD-13525

BiGG ID

2455100

Wikipedia Link

Retinal

METLIN ID

Not Available

PubChem Compound

6436079

PDB ID

Not Available

ChEBI ID

45487

Food Biomarker Ontology

Not Available

VMH ID

RETINAL_CIS_13

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Download (PDF)

General References

Hope WC, Patel BJ, Fiedler-Nagy C, Wittreich BH: Retinoids inhibit phospholipase A2 in human synovial fluid and arachidonic acid release from rat peritoneal macrophages. Inflammation. 1990 Oct;14(5):543-59. [PubMed:2123476 ]

Showing metabocard for 13-cis-Retinal (HMDB0006220)

MOL for HMDB0006220 (13-cis-Retinal)

3D MOL for HMDB0006220 (13-cis-Retinal)

3D SDF for HMDB0006220 (13-cis-Retinal)

3D-SDF for HMDB0006220 (13-cis-Retinal)

PDB for HMDB0006220 (13-cis-Retinal)

3D PDB for HMDB0006220 (13-cis-Retinal)

SMILES for HMDB0006220 (13-cis-Retinal)

INCHI for HMDB0006220 (13-cis-Retinal)

Structure for HMDB0006220 (13-cis-Retinal)

3D Structure for HMDB0006220 (13-cis-Retinal)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra