NP-MRD: Showing NP-Card for 9-cis-Retinal (NP0001490)

Jump To Section:

Identification Spectra BioTaxonomy ChemoTaxonomy Physical properties Links References XML

Record Information

Version

1.0

Created at

2007-05-22 17:52:59 UTC

Updated at

2021-06-30 02:06:15 UTC

NP-MRD ID

NP0001490

Secondary Accession Numbers

None

Natural Product 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>
NP0001490

> <DATABASE_NAME>
NP-MRD

> <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 NMR Assignments

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 Mass

284.4357 Da

Monoisotopic Mass

284.21402 Da

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

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, CDCl₃, experimental)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Anas platyrhynchos	FooDB	FooDB
Anatidae	FooDB	FooDB
Anser anser	FooDB	FooDB
Bison bison	FooDB	FooDB
Bos taurus	FooDB	FooDB
Bos taurus X Bison bison	FooDB	FooDB
Bubalus bubalis	FooDB	FooDB
Capra aegagrus hircus	FooDB	FooDB
Cervidae	FooDB	FooDB
Cervus canadensis	FooDB	FooDB
Columba	FooDB	FooDB
Columbidae	FooDB	FooDB
Dromaius novaehollandiae	FooDB	FooDB
Equus caballus	FooDB	FooDB
Gallus gallus	FooDB	FooDB
Lagopus muta	FooDB	FooDB
Leporidae	FooDB	FooDB
Lepus timidus	FooDB	FooDB
Melanitta fusca	FooDB	FooDB
Meleagris gallopavo	FooDB	FooDB
Numida meleagris	FooDB	FooDB
Odocoileus	FooDB	FooDB
Oryctolagus	FooDB	FooDB
Ovis aries	FooDB	FooDB
Phasianidae	FooDB	FooDB
Phasianus colchicus	FooDB	FooDB
Struthio camelus	FooDB	FooDB
Sus scrofa	FooDB	FooDB
Sus scrofa domestica	FooDB	FooDB

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 )

Physical Properties

State

Solid

Experimental 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

Predicted 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

External Links

HMDB ID

HMDB0006218

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB 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

Good Scents ID

Not Available

References

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 ]

Showing NP-Card for 9-cis-Retinal (NP0001490)

MOL for NP0001490 (9-cis-Retinal)

3D MOL for NP0001490 (9-cis-Retinal)

3D SDF for NP0001490 (9-cis-Retinal)

3D-SDF for NP0001490 (9-cis-Retinal)

PDB for NP0001490 (9-cis-Retinal)

3D PDB for NP0001490 (9-cis-Retinal)

SMILES for NP0001490 (9-cis-Retinal)

INCHI for NP0001490 (9-cis-Retinal)

Structure for NP0001490 (9-cis-Retinal)

3D Structure for NP0001490 (9-cis-Retinal)