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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2007-05-22 17:50:52 UTC

Update Date

2022-03-07 02:49:30 UTC

HMDB ID

HMDB0006217

Secondary Accession Numbers

HMDB06217

Metabolite Identification

Common Name

9-cis-Retinol

Description

9-cis-retinol is a retinoid. Retinoids (vitamin A and its analogs) are essential dietary substances that are needed by mammals for reproduction, normal embryogenesis, growth, vision, and maintaining normal cellular differentiation and the integrity of the immune system. Within cells, retinoids regulate gene transcription acting through ligand-dependent transcription factors, the retinoic acid receptors (RARs), and the retinoid X receptors (RXRs). All-trans-retinoic acid binds only to RARs with high affinity, whereas its 9-cis isomer binds with high affinity to both RARs and RXRs. The actions of all-trans- and 9-cis-retinoic acid in regulating cellular responses are distinct and not interchangeable. (PMID: 9115228 ).

Structure

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

HMDB0006217
     RDKit          3D
9-cis-Retinol
 51 51  0  0  0  0  0  0  0  0999 V2000
   -3.7114    1.4090    2.4036 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5328    0.1455    1.6468 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3597   -0.0727    1.0001 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3808    0.9584    1.1064 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1944    1.0105    0.5779 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6740    2.1719    0.8105 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1927    3.3095    1.6634 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8663    2.2173    0.2759 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4417    1.1703   -0.5712 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6634    1.3211   -1.0616 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3109    0.3059   -1.9256 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5243   -0.8876   -2.2303 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5307    0.5527   -2.3581 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2604   -0.3794   -3.2130 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6056    0.1944   -4.4526 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2993   -1.3504    0.3070 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9934   -1.8838   -0.1558 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2272   -1.2847   -0.8997 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8296   -2.4227    1.2902 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2776   -2.2340    1.5679 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6664   -0.7837    1.6294 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6949    1.4538    2.9028 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9576    1.5050    3.2215 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6230    2.3043    1.7572 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6273    1.8669    1.7214 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1362    0.2249   -0.0291 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1668    2.9275    2.6927 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9298    4.1272    1.6195 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7966    3.6856    1.3196 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4673    3.1176    0.4900 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9246    0.2604   -0.8264 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1923    2.2448   -0.8005 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8719   -1.5262   -3.0386 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2832   -1.4711   -1.2937 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5049   -0.5292   -2.5782 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0036    1.4787   -2.0673 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.2800   -0.6021   -2.7526 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8055   -1.3749   -3.3141 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7799   -0.5485   -5.1064 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7556   -1.4933   -1.1608 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1798   -1.8938    0.5730 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1489   -3.0167   -0.3930 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6705   -1.5071   -1.8366 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0593   -1.9845   -0.8263 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6427   -0.2631   -1.0484 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6843   -3.4382    0.8543 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1716   -2.3548    2.1737 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8741   -2.8145    0.8409 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4925   -2.6768    2.5800 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2581   -0.5680    0.6910 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3066   -0.6015    2.5245 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  1  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
 14 38  1  0
 15 39  1  0
 17 40  1  0
 17 41  1  0
 17 42  1  0
 18 43  1  0
 18 44  1  0
 18 45  1  0
 19 46  1  0
 19 47  1  0
 20 48  1  0
 20 49  1  0
 21 50  1  0
 21 51  1  0
M  END

  Mrv1652303192021392D          

 21 21  0  0  0  0            999 V2000
    2.4749   -1.0808    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4749   -1.9058    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1894   -2.3182    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1894   -0.6683    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9040   -1.9058    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9040   -1.0808    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500   -1.0808    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625   -0.3663    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1894    0.1568    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184   -0.6683    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9040    0.5692    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9040    1.3942    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1894    1.8067    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    1.8067    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    1.3942    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0473    1.8067    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7619    1.3942    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7619    0.5692    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4763    1.8067    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.1908    1.3942    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.9052    1.8067    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  4  1  0  0  0  0
  1  7  1  0  0  0  0
  1  8  1  0  0  0  0
  2  3  1  0  0  0  0
  3  5  1  0  0  0  0
  4  6  2  0  0  0  0
  4  9  1  0  0  0  0
  5  6  1  0  0  0  0
  6 10  1  0  0  0  0
  9 11  2  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 12 14  2  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 17 19  2  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0006217

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C20H30O/c1-16(8-6-9-17(2)13-15-21)11-12-19-18(3)10-7-14-20(19,4)5/h6,8-9,11-13,21H,7,10,14-15H2,1-5H3/b9-6+,12-11+,16-8-,17-13+

> <INCHI_KEY>
FPIPGXGPPPQFEQ-MKOSUFFBSA-N

> <FORMULA>
C20H30O

> <MOLECULAR_WEIGHT>
286.4516

> <EXACT_MASS>
286.229665582

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
51

> <JCHEM_AVERAGE_POLARIZABILITY>
35.864701839190474

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <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-tetraen-1-ol

> <ALOGPS_LOGP>
6.38

> <JCHEM_LOGP>
4.694093173000001

> <ALOGPS_LOGS>
-4.58

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
16.435769749539965

> <JCHEM_PKA_STRONGEST_BASIC>
-2.1707943115512176

> <JCHEM_POLAR_SURFACE_AREA>
20.23

> <JCHEM_REFRACTIVITY>
97.9234

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.58e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
9-cis-retinol

> <JCHEM_VEBER_RULE>
1

$$$$

HMDB0006217
     RDKit          3D
9-cis-Retinol
 51 51  0  0  0  0  0  0  0  0999 V2000
   -3.7114    1.4090    2.4036 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5328    0.1455    1.6468 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3597   -0.0727    1.0001 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3808    0.9584    1.1064 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1944    1.0105    0.5779 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6740    2.1719    0.8105 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1927    3.3095    1.6634 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8663    2.2173    0.2759 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4417    1.1703   -0.5712 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6634    1.3211   -1.0616 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3109    0.3059   -1.9256 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5243   -0.8876   -2.2303 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5307    0.5527   -2.3581 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2604   -0.3794   -3.2130 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6056    0.1944   -4.4526 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2993   -1.3504    0.3070 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9934   -1.8838   -0.1558 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2272   -1.2847   -0.8997 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8296   -2.4227    1.2902 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2776   -2.2340    1.5679 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6664   -0.7837    1.6294 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6949    1.4538    2.9028 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9576    1.5050    3.2215 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6230    2.3043    1.7572 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6273    1.8669    1.7214 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1362    0.2249   -0.0291 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1668    2.9275    2.6927 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9298    4.1272    1.6195 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7966    3.6856    1.3196 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4673    3.1176    0.4900 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9246    0.2604   -0.8264 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1923    2.2448   -0.8005 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8719   -1.5262   -3.0386 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2832   -1.4711   -1.2937 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5049   -0.5292   -2.5782 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0036    1.4787   -2.0673 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.2800   -0.6021   -2.7526 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8055   -1.3749   -3.3141 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7799   -0.5485   -5.1064 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7556   -1.4933   -1.1608 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1798   -1.8938    0.5730 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1489   -3.0167   -0.3930 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6705   -1.5071   -1.8366 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0593   -1.9845   -0.8263 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6427   -0.2631   -1.0484 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6843   -3.4382    0.8543 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1716   -2.3548    2.1737 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8741   -2.8145    0.8409 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4925   -2.6768    2.5800 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2581   -0.5680    0.6910 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3066   -0.6015    2.5245 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  1  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
 14 38  1  0
 15 39  1  0
 17 40  1  0
 17 41  1  0
 17 42  1  0
 18 43  1  0
 18 44  1  0
 18 45  1  0
 19 46  1  0
 19 47  1  0
 20 48  1  0
 20 49  1  0
 21 50  1  0
 21 51  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       4.620  -2.017   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.620  -3.557   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.954  -4.327   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.954  -1.247   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       7.287  -3.557   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       7.287  -2.017   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.080  -2.017   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.850  -0.684   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       5.954   0.293   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       8.621  -1.247   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       7.287   1.063   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       7.287   2.603   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.954   3.373   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       8.621   3.373   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       9.955   2.603   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      11.288   3.373   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      12.622   2.603   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      12.622   1.063   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      13.956   3.373   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      15.289   2.603   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      16.623   3.373   0.000  0.00  0.00           O+0
CONECT    1    2    4    7    8                                             
CONECT    2    1    3                                                       
CONECT    3    2    5                                                       
CONECT    4    1    6    9                                                  
CONECT    5    3    6                                                       
CONECT    6    4    5   10                                                  
CONECT    7    1                                                            
CONECT    8    1                                                            
CONECT    9    4   11                                                       
CONECT   10    6                                                            
CONECT   11    9   12                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20                                                            
MASTER        0    0    0    0    0    0    0    0   21    0   42    0
END

COMPND    HMDB0006217
HETATM    1  C1  UNL     1      -3.711   1.409   2.404  1.00  0.00           C  
HETATM    2  C2  UNL     1      -3.533   0.146   1.647  1.00  0.00           C  
HETATM    3  C3  UNL     1      -2.360  -0.073   1.000  1.00  0.00           C  
HETATM    4  C4  UNL     1      -1.381   0.958   1.106  1.00  0.00           C  
HETATM    5  C5  UNL     1      -0.194   1.010   0.578  1.00  0.00           C  
HETATM    6  C6  UNL     1       0.674   2.172   0.811  1.00  0.00           C  
HETATM    7  C7  UNL     1       0.193   3.309   1.663  1.00  0.00           C  
HETATM    8  C8  UNL     1       1.866   2.217   0.276  1.00  0.00           C  
HETATM    9  C9  UNL     1       2.442   1.170  -0.571  1.00  0.00           C  
HETATM   10  C10 UNL     1       3.663   1.321  -1.062  1.00  0.00           C  
HETATM   11  C11 UNL     1       4.311   0.306  -1.926  1.00  0.00           C  
HETATM   12  C12 UNL     1       3.524  -0.888  -2.230  1.00  0.00           C  
HETATM   13  C13 UNL     1       5.531   0.553  -2.358  1.00  0.00           C  
HETATM   14  C14 UNL     1       6.260  -0.379  -3.213  1.00  0.00           C  
HETATM   15  O1  UNL     1       6.606   0.194  -4.453  1.00  0.00           O  
HETATM   16  C15 UNL     1      -2.299  -1.350   0.307  1.00  0.00           C  
HETATM   17  C16 UNL     1      -0.993  -1.884  -0.156  1.00  0.00           C  
HETATM   18  C17 UNL     1      -3.227  -1.285  -0.900  1.00  0.00           C  
HETATM   19  C18 UNL     1      -2.830  -2.423   1.290  1.00  0.00           C  
HETATM   20  C19 UNL     1      -4.278  -2.234   1.568  1.00  0.00           C  
HETATM   21  C20 UNL     1      -4.666  -0.784   1.629  1.00  0.00           C  
HETATM   22  H1  UNL     1      -4.695   1.454   2.903  1.00  0.00           H  
HETATM   23  H2  UNL     1      -2.958   1.505   3.221  1.00  0.00           H  
HETATM   24  H3  UNL     1      -3.623   2.304   1.757  1.00  0.00           H  
HETATM   25  H4  UNL     1      -1.627   1.867   1.721  1.00  0.00           H  
HETATM   26  H5  UNL     1       0.136   0.225  -0.029  1.00  0.00           H  
HETATM   27  H6  UNL     1       0.167   2.927   2.693  1.00  0.00           H  
HETATM   28  H7  UNL     1       0.930   4.127   1.620  1.00  0.00           H  
HETATM   29  H8  UNL     1      -0.797   3.686   1.320  1.00  0.00           H  
HETATM   30  H9  UNL     1       2.467   3.118   0.490  1.00  0.00           H  
HETATM   31  H10 UNL     1       1.925   0.260  -0.826  1.00  0.00           H  
HETATM   32  H11 UNL     1       4.192   2.245  -0.801  1.00  0.00           H  
HETATM   33  H12 UNL     1       3.872  -1.526  -3.039  1.00  0.00           H  
HETATM   34  H13 UNL     1       3.283  -1.471  -1.294  1.00  0.00           H  
HETATM   35  H14 UNL     1       2.505  -0.529  -2.578  1.00  0.00           H  
HETATM   36  H15 UNL     1       6.004   1.479  -2.067  1.00  0.00           H  
HETATM   37  H16 UNL     1       7.280  -0.602  -2.753  1.00  0.00           H  
HETATM   38  H17 UNL     1       5.806  -1.375  -3.314  1.00  0.00           H  
HETATM   39  H18 UNL     1       6.780  -0.549  -5.106  1.00  0.00           H  
HETATM   40  H19 UNL     1      -0.756  -1.493  -1.161  1.00  0.00           H  
HETATM   41  H20 UNL     1      -0.180  -1.894   0.573  1.00  0.00           H  
HETATM   42  H21 UNL     1      -1.149  -3.017  -0.393  1.00  0.00           H  
HETATM   43  H22 UNL     1      -2.670  -1.507  -1.837  1.00  0.00           H  
HETATM   44  H23 UNL     1      -4.059  -1.985  -0.826  1.00  0.00           H  
HETATM   45  H24 UNL     1      -3.643  -0.263  -1.048  1.00  0.00           H  
HETATM   46  H25 UNL     1      -2.684  -3.438   0.854  1.00  0.00           H  
HETATM   47  H26 UNL     1      -2.172  -2.355   2.174  1.00  0.00           H  
HETATM   48  H27 UNL     1      -4.874  -2.814   0.841  1.00  0.00           H  
HETATM   49  H28 UNL     1      -4.493  -2.677   2.580  1.00  0.00           H  
HETATM   50  H29 UNL     1      -5.258  -0.568   0.691  1.00  0.00           H  
HETATM   51  H30 UNL     1      -5.307  -0.602   2.524  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   37   38
CONECT   15   39
CONECT   16   17   18   19
CONECT   17   40   41   42
CONECT   18   43   44   45
CONECT   19   20   46   47
CONECT   20   21   48   49
CONECT   21   50   51
END

HMDB0006217
     RDKit          3D
9-cis-Retinol
 51 51  0  0  0  0  0  0  0  0999 V2000
   -3.7114    1.4090    2.4036 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5328    0.1455    1.6468 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3597   -0.0727    1.0001 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3808    0.9584    1.1064 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1944    1.0105    0.5779 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6740    2.1719    0.8105 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1927    3.3095    1.6634 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8663    2.2173    0.2759 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4417    1.1703   -0.5712 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6634    1.3211   -1.0616 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3109    0.3059   -1.9256 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5243   -0.8876   -2.2303 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5307    0.5527   -2.3581 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2604   -0.3794   -3.2130 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6056    0.1944   -4.4526 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2993   -1.3504    0.3070 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9934   -1.8838   -0.1558 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2272   -1.2847   -0.8997 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8296   -2.4227    1.2902 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2776   -2.2340    1.5679 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6664   -0.7837    1.6294 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6949    1.4538    2.9028 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9576    1.5050    3.2215 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6230    2.3043    1.7572 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6273    1.8669    1.7214 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1362    0.2249   -0.0291 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1668    2.9275    2.6927 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9298    4.1272    1.6195 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7966    3.6856    1.3196 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4673    3.1176    0.4900 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9246    0.2604   -0.8264 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1923    2.2448   -0.8005 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8719   -1.5262   -3.0386 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2832   -1.4711   -1.2937 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5049   -0.5292   -2.5782 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0036    1.4787   -2.0673 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.2800   -0.6021   -2.7526 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8055   -1.3749   -3.3141 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7799   -0.5485   -5.1064 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7556   -1.4933   -1.1608 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1798   -1.8938    0.5730 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1489   -3.0167   -0.3930 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6705   -1.5071   -1.8366 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0593   -1.9845   -0.8263 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6427   -0.2631   -1.0484 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6843   -3.4382    0.8543 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1716   -2.3548    2.1737 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8741   -2.8145    0.8409 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4925   -2.6768    2.5800 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2581   -0.5680    0.6910 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3066   -0.6015    2.5245 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  1  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
 14 38  1  0
 15 39  1  0
 17 40  1  0
 17 41  1  0
 17 42  1  0
 18 43  1  0
 18 44  1  0
 18 45  1  0
 19 46  1  0
 19 47  1  0
 20 48  1  0
 20 49  1  0
 21 50  1  0
 21 51  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-tetraen-1-ol	ChEBI
(9cis)-Retinol	ChEBI
9-cis Retinol	HMDB

Chemical Formula

C₂₀H₃₀O

Average Molecular Weight

286.4516

Monoisotopic Molecular Weight

286.229665582

IUPAC Name

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

Traditional Name

9-cis-retinol

CAS Registry Number

22737-97-9

SMILES

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

InChI Identifier

InChI=1S/C20H30O/c1-16(8-6-9-17(2)13-15-21)11-12-19-18(3)10-7-14-20(19,4)5/h6,8-9,11-13,21H,7,10,14-15H2,1-5H3/b9-6+,12-11+,16-8-,17-13+

InChI Key

FPIPGXGPPPQFEQ-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
Fatty alcohol
Fatty acyl
Organic oxygen compound
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Alcohol
Aliphatic homomonocyclic compound

Molecular Framework

Aliphatic homomonocyclic compounds

External Descriptors

retinol (CHEBI:78272 )
Retinoids (C16682 )
Retinoids (LMPR01090009 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Source

Exogenous

Exogenous (HMDB: HMDB0006217)

Endogenous

Endogenous (HMDB: HMDB0006217)

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

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	0.0076 g/L	ALOGPS
logP	6.38	ALOGPS
logP	4.69	ChemAxon
logS	-4.6	ALOGPS
pKa (Strongest Acidic)	16.44	ChemAxon
pKa (Strongest Basic)	-2.2	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	1	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	20.23 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	97.92 m³·mol⁻¹	ChemAxon
Polarizability	35.86 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]+	176.396	31661259
DarkChem	[M-H]-	173.273	31661259
DeepCCS	[M+H]+	186.233	30932474
DeepCCS	[M-H]-	183.875	30932474
DeepCCS	[M-2H]-	217.551	30932474
DeepCCS	[M+Na]+	192.777	30932474
AllCCS	[M+H]+	174.3	32859911
AllCCS	[M+H-H2O]+	171.1	32859911
AllCCS	[M+NH4]+	177.3	32859911
AllCCS	[M+Na]+	178.2	32859911
AllCCS	[M-H]-	179.7	32859911
AllCCS	[M+Na-2H]-	180.4	32859911
AllCCS	[M+HCOO]-	181.3	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
9-cis-Retinol	C\C(=C/CO)\C=C\C=C(\C)/C=C/C1=C(C)CCCC1(C)C	3108.0	Standard polar	33892256
9-cis-Retinol	C\C(=C/CO)\C=C\C=C(\C)/C=C/C1=C(C)CCCC1(C)C	2431.2	Standard non polar	33892256
9-cis-Retinol	C\C(=C/CO)\C=C\C=C(\C)/C=C/C1=C(C)CCCC1(C)C	2417.0	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
9-cis-Retinol,1TMS,isomer #1	CC1=C(/C=C/C(C)=C\C=C\C(C)=C\CO[Si](C)(C)C)C(C)(C)CCC1	2597.7	Semi standard non polar	33892256
9-cis-Retinol,1TBDMS,isomer #1	CC1=C(/C=C/C(C)=C\C=C\C(C)=C\CO[Si](C)(C)C(C)(C)C)C(C)(C)CCC1	2794.8	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-Retinol GC-MS (Non-derivatized) - 70eV, Positive	splash10-00di-1190000000-346a3e44c44d46353e80	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 9-cis-Retinol GC-MS (1 TMS) - 70eV, Positive	splash10-0006-7139000000-7242603c3f7f12c824cd	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 9-cis-Retinol 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-Retinol 10V, Positive-QTOF	splash10-00kr-0490000000-97ed49d705440e4d32e7	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 9-cis-Retinol 20V, Positive-QTOF	splash10-00ks-3930000000-7c5bfbd8b838b97dc2aa	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 9-cis-Retinol 40V, Positive-QTOF	splash10-0fri-9820000000-6a49bab0c891ffe1e5b2	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 9-cis-Retinol 10V, Negative-QTOF	splash10-000i-0090000000-d0ff1cdc72141d0daa0e	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 9-cis-Retinol 20V, Negative-QTOF	splash10-0a4r-0090000000-c0a067ff8ed271b80945	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 9-cis-Retinol 40V, Negative-QTOF	splash10-00ku-4590000000-cfc35aba420e707075f7	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 9-cis-Retinol 10V, Negative-QTOF	splash10-0a4i-0090000000-fe93459d3069e264b77f	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 9-cis-Retinol 20V, Negative-QTOF	splash10-05mx-0190000000-f81760535f6050971f92	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 9-cis-Retinol 40V, Negative-QTOF	splash10-00li-0960000000-4dbc516b202b90a6c265	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 9-cis-Retinol 10V, Positive-QTOF	splash10-015i-1890000000-fb68e645ac6c84dc722c	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 9-cis-Retinol 20V, Positive-QTOF	splash10-05a9-2910000000-aa07b89a9cfe132b8725	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 9-cis-Retinol 40V, Positive-QTOF	splash10-06dl-5900000000-6de72efc591b252620c9	2021-09-22	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm
Extracellular
Membrane

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

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

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

FDB010848

KNApSAcK ID

Not Available

Chemspider ID

8123435

KEGG Compound ID

C16682

BioCyc ID

Not Available

BiGG ID

2265507

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

9947823

PDB ID

Not Available

ChEBI ID

78272

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Oediger, Hermann; Eiter, Karl. 9-cis-Vitamin A and its esters. (1963), 5 pp. DE 1157606 19631121 CAN 60:31181 AN 1964:31181

Material Safety Data Sheet (MSDS)

Not Available

General References

Mertz JR, Shang E, Piantedosi R, Wei S, Wolgemuth DJ, Blaner WS: Identification and characterization of a stereospecific human enzyme that catalyzes 9-cis-retinol oxidation. A possible role in 9-cis-retinoic acid formation. J Biol Chem. 1997 May 2;272(18):11744-9. [PubMed:9115228 ]

Showing metabocard for 9-cis-Retinol (HMDB0006217)

MOL for HMDB0006217 (9-cis-Retinol)

3D MOL for HMDB0006217 (9-cis-Retinol)

3D SDF for HMDB0006217 (9-cis-Retinol)

3D-SDF for HMDB0006217 (9-cis-Retinol)

PDB for HMDB0006217 (9-cis-Retinol)

3D PDB for HMDB0006217 (9-cis-Retinol)

SMILES for HMDB0006217 (9-cis-Retinol)

INCHI for HMDB0006217 (9-cis-Retinol)

Structure for HMDB0006217 (9-cis-Retinol)

3D Structure for HMDB0006217 (9-cis-Retinol)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra