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Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References enzymes (11) Show 11 proteins XML

Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2007-05-22 17:52:59 UTC

Update Date

2022-09-22 18:34:19 UTC

HMDB ID

HMDB0006218

Secondary Accession Numbers

HMDB06218

Metabolite Identification

Common Name

9-cis-Retinal

Description

In vivo, 9-cis-retinal is formed through oxidation of 9-cis-retinol by cis-retinol dehydrogenase (cRDH). (PMID:15572038 ). The generation of retinoic acid from retinol is a two-step reaction, with the rate-limiting step being the oxidation of retinol into the intermediate retinaldehyde. Two classes of. unrelated enzymes have been implicated in the oxidation of retinol, the classical cytosolic medium chain alcohol dehydrogenases and recently identified microsomal members of the short chain alcohol dehydrogenase reductase (SDR) superfamily. Further oxidation of the retinaldehyde to the retinoic acid is believed to be catalyzed by several cytosolic aldehyde dehydrogenases. Retinoids are micronutrients required to maintain and promote health of vertebrates. They act physiologically by participating in the visual cycle, in regulating cell differentiation, in embryonic development (PMID:10893430 ), in maintaining normal reproduction, and in the immune response (PMID:8882153 ). In non-ocular tissues, the effects of retinoids within the body are mediated through retinoic acid receptors (RARs) and retinoid X receptors (RXRs), which act to regulate gene expression as ligand-dependent transcription factors. The naturally occurring ligands for these nuclear receptors are thought to be all-trans-retinoic acid for RARs and 9-cis-retinoic acid for RXRs (PMID:10322133 ). While many details of the molecular actions of the RARs and RXRs in regulating gene transcription are understood (PMID:10418975 ), tissue-specific synthetic pathway(s) of their ligands has not been adequately defined. Nevertheless, the therapeutic efficacy of retinoids, including 9-cis-retinoic acid, is well established in both tissue culture and animal models of breast cancer (PMID:8825126 , PMID:12743994 ).

Structure

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

HMDB0006218
     RDKit          3D
9-cis-Retinal
 49 49  0  0  0  0  0  0  0  0999 V2000
   -2.1253   -1.7069   -3.4787 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1154   -0.6249   -3.4262 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5630   -0.2815   -2.2444 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0343   -1.0282   -1.1011 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7322   -0.9293    0.1691 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3397   -1.8125    1.1890 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3336   -2.8593    0.7660 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0165   -1.6818    2.4314 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0640   -0.6986    2.9479 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2241   -0.6050    4.2203 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1409    0.3162    4.8535 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9080    1.2736    4.0493 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3268    0.2987    6.1649 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2001    1.1551    6.9173 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9089    2.0566    6.4217 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4374    0.7584   -2.2761 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4056    0.8927   -1.1398 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2066    2.1443   -2.4652 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3429    0.5984   -3.5489 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4632    0.8348   -4.7256 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8004    0.0594   -4.6722 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6521   -2.6615   -3.1019 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0116   -1.5039   -2.8423 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4711   -1.8532   -4.5315 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7871   -1.8466   -1.2785 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0531   -0.1731    0.4553 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6333   -3.4094    1.6550 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2073   -2.2752    0.3874 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9484   -3.4744   -0.0579 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5112   -2.3787    3.1377 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4234   -0.0169    2.2967 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3078   -1.3270    4.8672 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4229    2.2906    3.9993 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9619    0.8488    2.9973 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9879    1.3377    4.3242 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7484   -0.4542    6.7398 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2495    1.0070    8.0099 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2792    1.5045   -1.5686 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7856   -0.0393   -0.7312 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9920    1.5770   -0.3844 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5559    2.8845   -2.7979 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0650    2.0936   -3.1516 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6035    2.5167   -1.4865 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8538   -0.3627   -3.5376 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0761    1.4159   -3.4709 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2321    1.9375   -4.8205 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0367    0.6164   -5.6712 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7393   -0.7401   -5.4725 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6421    0.7212   -5.0171 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


  Mrv1652303192021402D          

 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
    3.5724   -0.4125    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
    3.5724    1.2375    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
    4.2868    0.8250    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
    5.0013   -0.4125    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
    5.0013   -1.2375    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
    4.2868    0.0000    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
    5.7158   -1.6500    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>
HMDB0006218

> <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-MKOSUFFBSA-N

> <FORMULA>
C20H28O

> <MOLECULAR_WEIGHT>
284.4357

> <EXACT_MASS>
284.214015518

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
49

> <JCHEM_AVERAGE_POLARIZABILITY>
34.99087662948564

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

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

> <ALOGPS_LOGP>
6.62

> <JCHEM_LOGP>
4.855751458666667

> <ALOGPS_LOGS>
-4.83

> <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>
96.8654

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.20e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
9-cis-retinal

> <JCHEM_VEBER_RULE>
1

$$$$

HMDB0006218
     RDKit          3D
9-cis-Retinal
 49 49  0  0  0  0  0  0  0  0999 V2000
   -2.1253   -1.7069   -3.4787 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1154   -0.6249   -3.4262 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5630   -0.2815   -2.2444 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0343   -1.0282   -1.1011 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7322   -0.9293    0.1691 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3397   -1.8125    1.1890 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3336   -2.8593    0.7660 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0165   -1.6818    2.4314 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0640   -0.6986    2.9479 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2241   -0.6050    4.2203 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1409    0.3162    4.8535 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9080    1.2736    4.0493 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3268    0.2987    6.1649 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2001    1.1551    6.9173 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9089    2.0566    6.4217 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4374    0.7584   -2.2761 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4056    0.8927   -1.1398 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2066    2.1443   -2.4652 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3429    0.5984   -3.5489 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4632    0.8348   -4.7256 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8004    0.0594   -4.6722 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6521   -2.6615   -3.1019 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0116   -1.5039   -2.8423 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4711   -1.8532   -4.5315 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7871   -1.8466   -1.2785 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0531   -0.1731    0.4553 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6333   -3.4094    1.6550 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2073   -2.2752    0.3874 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9484   -3.4744   -0.0579 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5112   -2.3787    3.1377 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4234   -0.0169    2.2967 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3078   -1.3270    4.8672 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4229    2.2906    3.9993 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9619    0.8488    2.9973 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9879    1.3377    4.3242 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7484   -0.4542    6.7398 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2495    1.0070    8.0099 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2792    1.5045   -1.5686 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7856   -0.0393   -0.7312 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9920    1.5770   -0.3844 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5559    2.8845   -2.7979 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0650    2.0936   -3.1516 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6035    2.5167   -1.4865 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8538   -0.3627   -3.5376 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0761    1.4159   -3.4709 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2321    1.9375   -4.8205 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0367    0.6164   -5.6712 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7393   -0.7401   -5.4725 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6421    0.7212   -5.0171 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                                 19-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   19-MAR-20         0                                  
HETATM    1  C   UNK     0       5.335   6.160   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       6.668  -0.770   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       6.668   2.310   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       8.002   1.540   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       9.336  -0.770   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       9.336  -2.310   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       8.002   0.000   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      10.669  -3.080   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    HMDB0006218
HETATM    1  C1  UNL     1      -2.125  -1.707  -3.479  1.00  0.00           C  
HETATM    2  C2  UNL     1      -1.115  -0.625  -3.426  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.563  -0.281  -2.244  1.00  0.00           C  
HETATM    4  C4  UNL     1      -1.034  -1.028  -1.101  1.00  0.00           C  
HETATM    5  C5  UNL     1      -0.732  -0.929   0.169  1.00  0.00           C  
HETATM    6  C6  UNL     1      -1.340  -1.813   1.189  1.00  0.00           C  
HETATM    7  C7  UNL     1      -2.334  -2.859   0.766  1.00  0.00           C  
HETATM    8  C8  UNL     1      -1.016  -1.682   2.431  1.00  0.00           C  
HETATM    9  C9  UNL     1      -0.064  -0.699   2.948  1.00  0.00           C  
HETATM   10  C10 UNL     1       0.224  -0.605   4.220  1.00  0.00           C  
HETATM   11  C11 UNL     1       1.141   0.316   4.853  1.00  0.00           C  
HETATM   12  C12 UNL     1       1.908   1.274   4.049  1.00  0.00           C  
HETATM   13  C13 UNL     1       1.327   0.299   6.165  1.00  0.00           C  
HETATM   14  C14 UNL     1       2.200   1.155   6.917  1.00  0.00           C  
HETATM   15  O1  UNL     1       2.909   2.057   6.422  1.00  0.00           O  
HETATM   16  C15 UNL     1       0.437   0.758  -2.276  1.00  0.00           C  
HETATM   17  C16 UNL     1       1.406   0.893  -1.140  1.00  0.00           C  
HETATM   18  C17 UNL     1      -0.207   2.144  -2.465  1.00  0.00           C  
HETATM   19  C18 UNL     1       1.343   0.598  -3.549  1.00  0.00           C  
HETATM   20  C19 UNL     1       0.463   0.835  -4.726  1.00  0.00           C  
HETATM   21  C20 UNL     1      -0.800   0.059  -4.672  1.00  0.00           C  
HETATM   22  H1  UNL     1      -1.652  -2.661  -3.102  1.00  0.00           H  
HETATM   23  H2  UNL     1      -3.012  -1.504  -2.842  1.00  0.00           H  
HETATM   24  H3  UNL     1      -2.471  -1.853  -4.532  1.00  0.00           H  
HETATM   25  H4  UNL     1      -1.787  -1.847  -1.278  1.00  0.00           H  
HETATM   26  H5  UNL     1      -0.053  -0.173   0.455  1.00  0.00           H  
HETATM   27  H6  UNL     1      -2.633  -3.409   1.655  1.00  0.00           H  
HETATM   28  H7  UNL     1      -3.207  -2.275   0.387  1.00  0.00           H  
HETATM   29  H8  UNL     1      -1.948  -3.474  -0.058  1.00  0.00           H  
HETATM   30  H9  UNL     1      -1.511  -2.379   3.138  1.00  0.00           H  
HETATM   31  H10 UNL     1       0.423  -0.017   2.297  1.00  0.00           H  
HETATM   32  H11 UNL     1      -0.308  -1.327   4.867  1.00  0.00           H  
HETATM   33  H12 UNL     1       1.423   2.291   3.999  1.00  0.00           H  
HETATM   34  H13 UNL     1       1.962   0.849   2.997  1.00  0.00           H  
HETATM   35  H14 UNL     1       2.988   1.338   4.324  1.00  0.00           H  
HETATM   36  H15 UNL     1       0.748  -0.454   6.740  1.00  0.00           H  
HETATM   37  H16 UNL     1       2.249   1.007   8.010  1.00  0.00           H  
HETATM   38  H17 UNL     1       2.279   1.505  -1.569  1.00  0.00           H  
HETATM   39  H18 UNL     1       1.786  -0.039  -0.731  1.00  0.00           H  
HETATM   40  H19 UNL     1       0.992   1.577  -0.384  1.00  0.00           H  
HETATM   41  H20 UNL     1       0.556   2.885  -2.798  1.00  0.00           H  
HETATM   42  H21 UNL     1      -1.065   2.094  -3.152  1.00  0.00           H  
HETATM   43  H22 UNL     1      -0.603   2.517  -1.486  1.00  0.00           H  
HETATM   44  H23 UNL     1       1.854  -0.363  -3.538  1.00  0.00           H  
HETATM   45  H24 UNL     1       2.076   1.416  -3.471  1.00  0.00           H  
HETATM   46  H25 UNL     1       0.232   1.937  -4.821  1.00  0.00           H  
HETATM   47  H26 UNL     1       1.037   0.616  -5.671  1.00  0.00           H  
HETATM   48  H27 UNL     1      -0.739  -0.740  -5.472  1.00  0.00           H  
HETATM   49  H28 UNL     1      -1.642   0.721  -5.017  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

HMDB0006218
     RDKit          3D
9-cis-Retinal
 49 49  0  0  0  0  0  0  0  0999 V2000
   -2.1253   -1.7069   -3.4787 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1154   -0.6249   -3.4262 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5630   -0.2815   -2.2444 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0343   -1.0282   -1.1011 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7322   -0.9293    0.1691 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3397   -1.8125    1.1890 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3336   -2.8593    0.7660 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0165   -1.6818    2.4314 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0640   -0.6986    2.9479 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2241   -0.6050    4.2203 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1409    0.3162    4.8535 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9080    1.2736    4.0493 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3268    0.2987    6.1649 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2001    1.1551    6.9173 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9089    2.0566    6.4217 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4374    0.7584   -2.2761 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4056    0.8927   -1.1398 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2066    2.1443   -2.4652 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3429    0.5984   -3.5489 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4632    0.8348   -4.7256 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8004    0.0594   -4.6722 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6521   -2.6615   -3.1019 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0116   -1.5039   -2.8423 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4711   -1.8532   -4.5315 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7871   -1.8466   -1.2785 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0531   -0.1731    0.4553 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6333   -3.4094    1.6550 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2073   -2.2752    0.3874 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9484   -3.4744   -0.0579 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5112   -2.3787    3.1377 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4234   -0.0169    2.2967 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3078   -1.3270    4.8672 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4229    2.2906    3.9993 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9619    0.8488    2.9973 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9879    1.3377    4.3242 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7484   -0.4542    6.7398 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2495    1.0070    8.0099 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2792    1.5045   -1.5686 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7856   -0.0393   -0.7312 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9920    1.5770   -0.3844 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5559    2.8845   -2.7979 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0650    2.0936   -3.1516 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6035    2.5167   -1.4865 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8538   -0.3627   -3.5376 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0761    1.4159   -3.4709 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2321    1.9375   -4.8205 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0367    0.6164   -5.6712 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7393   -0.7401   -5.4725 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6421    0.7212   -5.0171 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
(2E,4E,6Z,8E)-3,7-Dimethyl-9-(2,6,6-trimethylcyclohex-1-en-1-yl)nona-2,4,6,8-tetraenal	ChEBI
(9cis)-Retinal	ChEBI
9-C-Retinal	ChEBI
9-cis-3,7-Dimethyl-9-(2,6,6-trimethyl-1-cyclohexen-1-yl)-2,4,6,8-nonatetraenal	ChEBI
9-cis-7,11,13-trans-Retinal	ChEBI
9-cis-Retinaldehyde	ChEBI
9-cis-Vitamin a aldehyde	ChEBI
Isoretinene a	ChEBI
cis-9-Retinal	HMDB

Chemical Formula

C₂₀H₂₈O

Average Molecular Weight

284.4357

Monoisotopic Molecular Weight

284.214015518

IUPAC Name

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

Traditional Name

9-cis-retinal

CAS Registry Number

514-85-2

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-MKOSUFFBSA-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:78273 )
Retinoids (C16681 )
Retinoids (LMPR01090017 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Source

Exogenous

Exogenous (HMDB: HMDB0006218)

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: HMDB0006218)

Process

Naturally occurring process

Biological process

Biochemical pathway

Metabolic pathway

Retinol Metabolism (PathBank: SMP0087353)

Disease pathway

Vitamin A Deficiency (PathBank: SMP0120500)

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

Experimental Collision Cross Sections

Adduct Type	Data Source	CCS Value (Å²)	Reference
[M+H]+	MetCCS_train_pos	170.135	30932474
[M+H]+	Not Available	170.471	http://allccs.zhulab.cn/database/detail?ID=AllCCS00000455

Predicted Molecular Properties

Property	Value	Source
Water Solubility	0.0042 g/L	ALOGPS
logP	6.62	ALOGPS
logP	4.86	ChemAxon
logS	-4.8	ALOGPS
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	34.99 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]+	173.938	31661259
DarkChem	[M-H]-	174.202	31661259
DeepCCS	[M+H]+	181.622	30932474
DeepCCS	[M-H]-	179.264	30932474
DeepCCS	[M-2H]-	212.963	30932474
DeepCCS	[M+Na]+	188.189	30932474
AllCCS	[M+H]+	174.5	32859911
AllCCS	[M+H-H2O]+	171.3	32859911
AllCCS	[M+NH4]+	177.5	32859911
AllCCS	[M+Na]+	178.4	32859911
AllCCS	[M-H]-	178.3	32859911
AllCCS	[M+Na-2H]-	178.9	32859911
AllCCS	[M+HCOO]-	179.7	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
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.	8.21 minutes	32390414
Predicted by Siyang on May 30, 2022	27.1501 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	1.5 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	3428.0 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	881.0 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	341.3 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	576.7 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	337.9 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	1067.2 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	1039.8 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	101.8 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	2311.8 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	761.2 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	1747.1 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	924.4 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	605.9 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	594.5 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	867.4 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	8.5 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
9-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
9-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
9-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 - 9-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 - 9-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 - 9-cis-Retinal 10V, Positive-QTOF	splash10-000i-1490000000-97cddfba9819c3417386	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 9-cis-Retinal 20V, Positive-QTOF	splash10-001s-3920000000-0be8a19c3cba33e3b06b	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 9-cis-Retinal 40V, Positive-QTOF	splash10-0kui-9720000000-a579102a9f5600032e3f	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 9-cis-Retinal 10V, Negative-QTOF	splash10-001i-0090000000-e7d5d678e91ec531c2ae	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 9-cis-Retinal 20V, Negative-QTOF	splash10-0a59-0090000000-8af2668c966a1c8a3cef	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 9-cis-Retinal 40V, Negative-QTOF	splash10-00ku-3690000000-54506b9021b67caed041	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 9-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 - 9-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 - 9-cis-Retinal 40V, Positive-QTOF	splash10-052f-7900000000-d2bb7c1aeeb87d8833d2	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 9-cis-Retinal 10V, Negative-QTOF	splash10-0a59-0090000000-2ec2f8f314943441fa15	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 9-cis-Retinal 20V, Negative-QTOF	splash10-0pb9-0190000000-312cebb17ccd0189ab4d	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 9-cis-Retinal 40V, Negative-QTOF	splash10-000i-1590000000-b2551eac481c0c930a4d	2021-09-23	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

Blood
Urine

Tissue Locations

Not Available

Pathways

Name	SMPDB/PathBank	KEGG
Retinol Metabolism
Vitamin A Deficiency		Not Available

Normal Concentrations

Not Available

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Cancer patients undergoing total body irradiation	31424920	details
Urine	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Cancer patients undergoing total body irradiation	31424920	details

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

FDB023842

KNApSAcK ID

Not Available

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

6436082

PDB ID

Not Available

ChEBI ID

78273

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Ostapenko, I. A.; Furaev, V. V. The 9-cis isomerization of all-trans-retinal during in vitro regeneration of visual pigment. Nature (London), New Biology (1973), 243(127), 185-6.

Material Safety Data Sheet (MSDS)

Not Available

General References

Paik J, Blaner WS, Swisshelm K: Cis-retinol dehydrogenase: 9-cis-retinol metabolism and its effect on proliferation of human MCF7 breast cancer cells. Exp Cell Res. 2005 Feb 1;303(1):183-96. [PubMed:15572038 ]
Ross SA, McCaffery PJ, Drager UC, De Luca LM: Retinoids in embryonal development. Physiol Rev. 2000 Jul;80(3):1021-54. [PubMed:10893430 ]
Glass CK: Some new twists in the regulation of gene expression by thyroid hormone and retinoic acid receptors. J Endocrinol. 1996 Sep;150(3):349-57. [PubMed:8882153 ]
Xu L, Glass CK, Rosenfeld MG: Coactivator and corepressor complexes in nuclear receptor function. Curr Opin Genet Dev. 1999 Apr;9(2):140-7. [PubMed:10322133 ]
McKenna NJ, Xu J, Nawaz Z, Tsai SY, Tsai MJ, O'Malley BW: Nuclear receptor coactivators: multiple enzymes, multiple complexes, multiple functions. J Steroid Biochem Mol Biol. 1999 Apr-Jun;69(1-6):3-12. [PubMed:10418975 ]
Gottardis MM, Lamph WW, Shalinsky DR, Wellstein A, Heyman RA: The efficacy of 9-cis retinoic acid in experimental models of cancer. Breast Cancer Res Treat. 1996;38(1):85-96. [PubMed:8825126 ]
Paik J, Blaner WS, Sommer KM, Moe R, Swisshlem K: Retinoids, retinoic acid receptors, and breast cancer. Cancer Invest. 2003 Apr;21(2):304-12. [PubMed:12743994 ]

Only showing the first 10 proteins. There are 11 proteins in total.

Show all enzymes and transporters

Enzymes

Enzyme Details

1. Retinal dehydrogenase 1

General function:: Involved in oxidoreductase activity
Specific function:: Binds free retinal and cellular retinol-binding protein-bound retinal. Can convert/oxidize retinaldehyde to retinoic acid (By similarity).
Gene Name:: ALDH1A1
Uniprot ID:: P00352
Molecular weight:: 54861.44

Reactions

9-cis-Retinal + NAD + Water → 9-cis-Retinoic acid + NADH + Hydrogen Ion	details

Enzyme Details

2. Retinal dehydrogenase 2

General function:: Involved in oxidoreductase activity
Specific function:: Recognizes as substrates free retinal and cellular retinol-binding protein-bound retinal. Does metabolize octanal and decanal but does not metabolize citral, benzaldehyde, acetaldehyde and propanal efficiently (By similarity).
Gene Name:: ALDH1A2
Uniprot ID:: O94788
Molecular weight:: 54672.24

Reactions

9-cis-Retinal + NAD + Water → 9-cis-Retinoic acid + NADH + Hydrogen Ion	details

Enzyme Details

3. Alcohol dehydrogenase class-3

General function:: Involved in zinc ion binding
Specific function:: Class-III ADH is remarkably ineffective in oxidizing ethanol, but it readily catalyzes the oxidation of long-chain primary alcohols and the oxidation of S-(hydroxymethyl) glutathione.
Gene Name:: ADH5
Uniprot ID:: P11766
Molecular weight:: 39723.945

Enzyme Details

4. Alcohol dehydrogenase 1B

General function:: Involved in zinc ion binding
Specific function:: Not Available
Gene Name:: ADH1B
Uniprot ID:: P00325
Molecular weight:: 39835.17

Enzyme Details

5. Alcohol dehydrogenase class 4 mu/sigma chain

General function:: Involved in zinc ion binding
Specific function:: Could function in retinol oxidation for the synthesis of retinoic acid, a hormone important for cellular differentiation. Medium-chain (octanol) and aromatic (m-nitrobenzaldehyde) compounds are the best substrates. Ethanol is not a good substrate but at the high ethanol concentrations reached in the digestive tract, it plays a role in the ethanol oxidation and contributes to the first pass ethanol metabolism.
Gene Name:: ADH7
Uniprot ID:: P40394
Molecular weight:: 41480.985

Enzyme Details

6. Alcohol dehydrogenase 1A

General function:: Involved in zinc ion binding
Specific function:: Not Available
Gene Name:: ADH1A
Uniprot ID:: P07327
Molecular weight:: 39858.37

Enzyme Details

7. Alcohol dehydrogenase 6

General function:: Involved in zinc ion binding
Specific function:: Not Available
Gene Name:: ADH6
Uniprot ID:: P28332
Molecular weight:: 39072.275

Enzyme Details

8. Alcohol dehydrogenase 1C

General function:: Involved in zinc ion binding
Specific function:: Not Available
Gene Name:: ADH1C
Uniprot ID:: P00326
Molecular weight:: 39867.27

Enzyme Details

9. Beta,beta-carotene 15,15'-monooxygenase

General function:: Secondary metabolites biosynthesis, transport and catabolism
Specific function:: Symmetrically cleaves beta-carotene into two molecules of retinal. The reaction proceeds in three stages, epoxidation of the 15,15'-double bond, hydration of the double bond leading to ring opening, and oxidative cleavage of the diol formed.
Gene Name:: BCMO1
Uniprot ID:: Q9HAY6
Molecular weight:: 62636.69

Enzyme Details

10. Aldehyde dehydrogenase family 8 member A1

General function:: Involved in oxidoreductase activity
Specific function:: Converts 9-cis-retinal to 9-cis-retinoic acid. Has lower activity towards 13-cis-retinal. Has much lower activity towards all-trans-retinal. Has highest activity with benzaldehyde and decanal (in vitro). Has a preference for NAD, but shows considerable activity with NADP (in vitro)
Gene Name:: ALDH8A1
Uniprot ID:: Q9H2A2
Molecular weight:: 53400.9

Only showing the first 10 proteins. There are 11 proteins in total.

Show all enzymes and transporters

Showing metabocard for 9-cis-Retinal (HMDB0006218)

MOL for HMDB0006218 (9-cis-Retinal)

3D MOL for HMDB0006218 (9-cis-Retinal)

3D SDF for HMDB0006218 (9-cis-Retinal)

3D-SDF for HMDB0006218 (9-cis-Retinal)

PDB for HMDB0006218 (9-cis-Retinal)

3D PDB for HMDB0006218 (9-cis-Retinal)

SMILES for HMDB0006218 (9-cis-Retinal)

INCHI for HMDB0006218 (9-cis-Retinal)

Structure for HMDB0006218 (9-cis-Retinal)

3D Structure for HMDB0006218 (9-cis-Retinal)

Experimental Collision Cross Sections

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

Enzymes

Reactions

Reactions