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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2009-07-25 00:09:00 UTC

Update Date

2022-03-07 02:51:27 UTC

HMDB ID

HMDB0012874

Secondary Accession Numbers

HMDB12874

Metabolite Identification

Common Name

9,13-cis-Retinoic acid

Description

9,13-cis-Retinoic acid 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. 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).

Structure

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

HMDB0012874
     RDKit          3D
9,13-cis-Retinoic acid
 50 50  0  0  0  0  0  0  0  0999 V2000
   -3.1680   -0.4619   -3.2530 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2013   -1.0235   -1.8600 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1614   -0.7874   -1.0527 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0605    0.0022   -1.5794 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0348    0.3373   -0.9489 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0757    1.1371   -1.5835 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9352    1.6066   -2.9784 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1651    1.4547   -0.9161 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4136    1.0568    0.4418 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5435    1.4246    1.0358 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8043    1.0307    2.4003 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8035    0.2048    3.1560 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9201    1.3918    2.9922 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9759    2.1799    2.4080 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9808    2.4117    3.1805 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0524    2.7136    1.1440 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0784   -1.2873    0.3353 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8857   -2.1922    0.4826 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9787   -0.0963    1.2778 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2973   -2.0728    0.7826 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5597   -1.6516    0.0967 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3355   -1.8031   -1.3961 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1747    0.6297   -3.2460 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2589   -0.9064   -3.7219 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0342   -0.8902   -3.7947 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1189    0.3796   -2.6257 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1538    0.0089    0.0573 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7517    0.7352   -3.6353 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7619    2.2394   -3.2944 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0132    2.2188   -3.0047 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9466    2.0680   -1.4252 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7206    0.4684    1.0074 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2205    2.0046    0.4701 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9155    0.8089    3.3574 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6020   -0.6881    2.5248 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2440   -0.1711    4.1015 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0345    1.0402    4.0490 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1949    3.7336    1.0926 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2674   -3.2500    0.6122 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2374   -1.9141    1.3183 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2956   -2.2103   -0.4679 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9185    0.8530    0.7106 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1390   -0.2102    1.9888 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8870   -0.0471    1.9521 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3661   -1.9710    1.8840 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0997   -3.1399    0.5676 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3426   -2.3891    0.3681 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8838   -0.6455    0.3734 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2231   -2.9089   -1.5839 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2641   -1.4221   -1.8865 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
 14 16  1  0
  3 17  1  0
 17 18  1  0
 17 19  1  0
 17 20  1  0
 20 21  1  0
 21 22  1  0
 22  2  1  0
  1 23  1  0
  1 24  1  0
  1 25  1  0
  4 26  1  0
  5 27  1  0
  7 28  1  0
  7 29  1  0
  7 30  1  0
  8 31  1  0
  9 32  1  0
 10 33  1  0
 12 34  1  0
 12 35  1  0
 12 36  1  0
 13 37  1  0
 16 38  1  0
 18 39  1  0
 18 40  1  0
 18 41  1  0
 19 42  1  0
 19 43  1  0
 19 44  1  0
 20 45  1  0
 20 46  1  0
 21 47  1  0
 21 48  1  0
 22 49  1  0
 22 50  1  0
M  END

6419708
  Mrv1652305281820312D          

 22 22  0  0  0  0            999 V2000
    8.8777   -1.7473    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.1633   -0.5099    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4474    1.1401    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7329    0.7276    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7329   -0.0973    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1618    0.7276    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4473   -0.5098    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1618   -0.0973    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0349    1.8546    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8599    1.8546    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8763    1.1401    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8764   -0.5098    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5908    0.7276    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3053    1.1401    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3053    1.9651    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0198    0.7276    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0198   -0.0973    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7343   -0.5098    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7343   -1.3349    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0198   -1.7474    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4488   -1.7474    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.1633   -1.3349    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1 22  1  0  0  0  0
  2 22  2  0  0  0  0
  3  4  1  0  0  0  0
  3  6  1  0  0  0  0
  3  9  1  0  0  0  0
  3 10  1  0  0  0  0
  4  5  1  0  0  0  0
  5  7  1  0  0  0  0
  6  8  2  0  0  0  0
  6 11  1  0  0  0  0
  7  8  1  0  0  0  0
  8 12  1  0  0  0  0
 11 13  2  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 14 16  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 19 21  2  0  0  0  0
 21 22  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0012874

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C20H28O2/c1-15(8-6-9-16(2)14-19(21)22)11-12-18-17(3)10-7-13-20(18,4)5/h6,8-9,11-12,14H,7,10,13H2,1-5H3,(H,21,22)/b9-6+,12-11+,15-8-,16-14-

> <INCHI_KEY>
SHGAZHPCJJPHSC-CDMOMSTLSA-N

> <FORMULA>
C20H28O2

> <MOLECULAR_WEIGHT>
300.4351

> <EXACT_MASS>
300.20893014

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
50

> <JCHEM_AVERAGE_POLARIZABILITY>
35.86837717218032

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

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

> <ALOGPS_LOGP>
5.66

> <JCHEM_LOGP>
5.014367711

> <ALOGPS_LOGS>
-4.80

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.996647744997455

> <JCHEM_POLAR_SURFACE_AREA>
37.3

> <JCHEM_REFRACTIVITY>
97.79079999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
4.77e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
9,13-di-cis-retinoic acid

> <JCHEM_VEBER_RULE>
1

$$$$

HMDB0012874
     RDKit          3D
9,13-cis-Retinoic acid
 50 50  0  0  0  0  0  0  0  0999 V2000
   -3.1680   -0.4619   -3.2530 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2013   -1.0235   -1.8600 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1614   -0.7874   -1.0527 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0605    0.0022   -1.5794 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0348    0.3373   -0.9489 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0757    1.1371   -1.5835 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9352    1.6066   -2.9784 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1651    1.4547   -0.9161 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4136    1.0568    0.4418 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5435    1.4246    1.0358 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8043    1.0307    2.4003 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8035    0.2048    3.1560 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9201    1.3918    2.9922 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9759    2.1799    2.4080 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9808    2.4117    3.1805 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0524    2.7136    1.1440 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0784   -1.2873    0.3353 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8857   -2.1922    0.4826 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9787   -0.0963    1.2778 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2973   -2.0728    0.7826 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5597   -1.6516    0.0967 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3355   -1.8031   -1.3961 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1747    0.6297   -3.2460 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2589   -0.9064   -3.7219 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0342   -0.8902   -3.7947 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1189    0.3796   -2.6257 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1538    0.0089    0.0573 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7517    0.7352   -3.6353 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7619    2.2394   -3.2944 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0132    2.2188   -3.0047 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9466    2.0680   -1.4252 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7206    0.4684    1.0074 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2205    2.0046    0.4701 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9155    0.8089    3.3574 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6020   -0.6881    2.5248 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2440   -0.1711    4.1015 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0345    1.0402    4.0490 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1949    3.7336    1.0926 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2674   -3.2500    0.6122 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2374   -1.9141    1.3183 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2956   -2.2103   -0.4679 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9185    0.8530    0.7106 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1390   -0.2102    1.9888 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8870   -0.0471    1.9521 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3661   -1.9710    1.8840 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0997   -3.1399    0.5676 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3426   -2.3891    0.3681 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8838   -0.6455    0.3734 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2231   -2.9089   -1.5839 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2641   -1.4221   -1.8865 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
 14 16  1  0
  3 17  1  0
 17 18  1  0
 17 19  1  0
 17 20  1  0
 20 21  1  0
 21 22  1  0
 22  2  1  0
  1 23  1  0
  1 24  1  0
  1 25  1  0
  4 26  1  0
  5 27  1  0
  7 28  1  0
  7 29  1  0
  7 30  1  0
  8 31  1  0
  9 32  1  0
 10 33  1  0
 12 34  1  0
 12 35  1  0
 12 36  1  0
 13 37  1  0
 16 38  1  0
 18 39  1  0
 18 40  1  0
 18 41  1  0
 19 42  1  0
 19 43  1  0
 19 44  1  0
 20 45  1  0
 20 46  1  0
 21 47  1  0
 21 48  1  0
 22 49  1  0
 22 50  1  0
M  END

HEADER    PROTEIN                                 28-MAY-18   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 6419708                                           
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-MAY-18         0                                  
HETATM    1  O   UNK     0      16.572  -3.262   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      15.238  -0.952   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       4.568   2.128   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.235   1.358   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.235  -0.182   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.902   1.358   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.568  -0.952   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       5.902  -0.182   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.798   3.462   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       5.338   3.462   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       7.236   2.128   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       7.236  -0.952   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       8.569   1.358   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       9.903   2.128   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       9.903   3.668   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      11.237   1.358   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      11.237  -0.182   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      12.571  -0.952   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      12.571  -2.492   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      11.237  -3.262   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      13.904  -3.262   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      15.238  -2.492   0.000  0.00  0.00           C+0
CONECT    1   22                                                            
CONECT    2   22                                                            
CONECT    3    4    6    9   10                                             
CONECT    4    3    5                                                       
CONECT    5    4    7                                                       
CONECT    6    3    8   11                                                  
CONECT    7    5    8                                                       
CONECT    8    6    7   12                                                  
CONECT    9    3                                                            
CONECT   10    3                                                            
CONECT   11    6   13                                                       
CONECT   12    8                                                            
CONECT   13   11   14                                                       
CONECT   14   13   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19   22                                                       
CONECT   22    1    2   21                                                  
MASTER        0    0    0    0    0    0    0    0   22    0   44    0
END

COMPND    HMDB0012874
HETATM    1  C1  UNL     1      -3.168  -0.462  -3.253  1.00  0.00           C  
HETATM    2  C2  UNL     1      -3.201  -1.024  -1.860  1.00  0.00           C  
HETATM    3  C3  UNL     1      -2.161  -0.787  -1.053  1.00  0.00           C  
HETATM    4  C4  UNL     1      -1.061   0.002  -1.579  1.00  0.00           C  
HETATM    5  C5  UNL     1       0.035   0.337  -0.949  1.00  0.00           C  
HETATM    6  C6  UNL     1       1.076   1.137  -1.583  1.00  0.00           C  
HETATM    7  C7  UNL     1       0.935   1.607  -2.978  1.00  0.00           C  
HETATM    8  C8  UNL     1       2.165   1.455  -0.916  1.00  0.00           C  
HETATM    9  C9  UNL     1       2.414   1.057   0.442  1.00  0.00           C  
HETATM   10  C10 UNL     1       3.543   1.425   1.036  1.00  0.00           C  
HETATM   11  C11 UNL     1       3.804   1.031   2.400  1.00  0.00           C  
HETATM   12  C12 UNL     1       2.803   0.205   3.156  1.00  0.00           C  
HETATM   13  C13 UNL     1       4.920   1.392   2.992  1.00  0.00           C  
HETATM   14  C14 UNL     1       5.976   2.180   2.408  1.00  0.00           C  
HETATM   15  O1  UNL     1       6.981   2.412   3.181  1.00  0.00           O  
HETATM   16  O2  UNL     1       6.052   2.714   1.144  1.00  0.00           O  
HETATM   17  C15 UNL     1      -2.078  -1.287   0.335  1.00  0.00           C  
HETATM   18  C16 UNL     1      -0.886  -2.192   0.483  1.00  0.00           C  
HETATM   19  C17 UNL     1      -1.979  -0.096   1.278  1.00  0.00           C  
HETATM   20  C18 UNL     1      -3.297  -2.073   0.783  1.00  0.00           C  
HETATM   21  C19 UNL     1      -4.560  -1.652   0.097  1.00  0.00           C  
HETATM   22  C20 UNL     1      -4.336  -1.803  -1.396  1.00  0.00           C  
HETATM   23  H1  UNL     1      -3.175   0.630  -3.246  1.00  0.00           H  
HETATM   24  H2  UNL     1      -2.259  -0.906  -3.722  1.00  0.00           H  
HETATM   25  H3  UNL     1      -4.034  -0.890  -3.795  1.00  0.00           H  
HETATM   26  H4  UNL     1      -1.119   0.380  -2.626  1.00  0.00           H  
HETATM   27  H5  UNL     1       0.154   0.009   0.057  1.00  0.00           H  
HETATM   28  H6  UNL     1       0.752   0.735  -3.635  1.00  0.00           H  
HETATM   29  H7  UNL     1       1.762   2.239  -3.294  1.00  0.00           H  
HETATM   30  H8  UNL     1      -0.013   2.219  -3.005  1.00  0.00           H  
HETATM   31  H9  UNL     1       2.947   2.068  -1.425  1.00  0.00           H  
HETATM   32  H10 UNL     1       1.721   0.468   1.007  1.00  0.00           H  
HETATM   33  H11 UNL     1       4.220   2.005   0.470  1.00  0.00           H  
HETATM   34  H12 UNL     1       1.915   0.809   3.357  1.00  0.00           H  
HETATM   35  H13 UNL     1       2.602  -0.688   2.525  1.00  0.00           H  
HETATM   36  H14 UNL     1       3.244  -0.171   4.102  1.00  0.00           H  
HETATM   37  H15 UNL     1       5.034   1.040   4.049  1.00  0.00           H  
HETATM   38  H16 UNL     1       6.195   3.734   1.093  1.00  0.00           H  
HETATM   39  H17 UNL     1      -1.267  -3.250   0.612  1.00  0.00           H  
HETATM   40  H18 UNL     1      -0.237  -1.914   1.318  1.00  0.00           H  
HETATM   41  H19 UNL     1      -0.296  -2.210  -0.468  1.00  0.00           H  
HETATM   42  H20 UNL     1      -1.919   0.853   0.711  1.00  0.00           H  
HETATM   43  H21 UNL     1      -1.139  -0.210   1.989  1.00  0.00           H  
HETATM   44  H22 UNL     1      -2.887  -0.047   1.952  1.00  0.00           H  
HETATM   45  H23 UNL     1      -3.366  -1.971   1.884  1.00  0.00           H  
HETATM   46  H24 UNL     1      -3.100  -3.140   0.568  1.00  0.00           H  
HETATM   47  H25 UNL     1      -5.343  -2.389   0.368  1.00  0.00           H  
HETATM   48  H26 UNL     1      -4.884  -0.646   0.373  1.00  0.00           H  
HETATM   49  H27 UNL     1      -4.223  -2.909  -1.584  1.00  0.00           H  
HETATM   50  H28 UNL     1      -5.264  -1.422  -1.886  1.00  0.00           H  
CONECT    1    2   23   24   25
CONECT    2    3    3   22
CONECT    3    4   17
CONECT    4    5    5   26
CONECT    5    6   27
CONECT    6    7    8    8
CONECT    7   28   29   30
CONECT    8    9   31
CONECT    9   10   10   32
CONECT   10   11   33
CONECT   11   12   13   13
CONECT   12   34   35   36
CONECT   13   14   37
CONECT   14   15   15   16
CONECT   16   38
CONECT   17   18   19   20
CONECT   18   39   40   41
CONECT   19   42   43   44
CONECT   20   21   45   46
CONECT   21   22   47   48
CONECT   22   49   50
END

HMDB0012874
     RDKit          3D
9,13-cis-Retinoic acid
 50 50  0  0  0  0  0  0  0  0999 V2000
   -3.1680   -0.4619   -3.2530 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2013   -1.0235   -1.8600 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1614   -0.7874   -1.0527 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0605    0.0022   -1.5794 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0348    0.3373   -0.9489 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0757    1.1371   -1.5835 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9352    1.6066   -2.9784 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1651    1.4547   -0.9161 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4136    1.0568    0.4418 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5435    1.4246    1.0358 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8043    1.0307    2.4003 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8035    0.2048    3.1560 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9201    1.3918    2.9922 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9759    2.1799    2.4080 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9808    2.4117    3.1805 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0524    2.7136    1.1440 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0784   -1.2873    0.3353 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8857   -2.1922    0.4826 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9787   -0.0963    1.2778 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2973   -2.0728    0.7826 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5597   -1.6516    0.0967 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3355   -1.8031   -1.3961 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1747    0.6297   -3.2460 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2589   -0.9064   -3.7219 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0342   -0.8902   -3.7947 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1189    0.3796   -2.6257 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1538    0.0089    0.0573 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7517    0.7352   -3.6353 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7619    2.2394   -3.2944 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0132    2.2188   -3.0047 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9466    2.0680   -1.4252 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7206    0.4684    1.0074 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2205    2.0046    0.4701 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9155    0.8089    3.3574 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6020   -0.6881    2.5248 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2440   -0.1711    4.1015 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0345    1.0402    4.0490 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1949    3.7336    1.0926 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2674   -3.2500    0.6122 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2374   -1.9141    1.3183 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2956   -2.2103   -0.4679 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9185    0.8530    0.7106 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1390   -0.2102    1.9888 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8870   -0.0471    1.9521 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3661   -1.9710    1.8840 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0997   -3.1399    0.5676 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3426   -2.3891    0.3681 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8838   -0.6455    0.3734 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2231   -2.9089   -1.5839 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2641   -1.4221   -1.8865 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
 14 16  1  0
  3 17  1  0
 17 18  1  0
 17 19  1  0
 17 20  1  0
 20 21  1  0
 21 22  1  0
 22  2  1  0
  1 23  1  0
  1 24  1  0
  1 25  1  0
  4 26  1  0
  5 27  1  0
  7 28  1  0
  7 29  1  0
  7 30  1  0
  8 31  1  0
  9 32  1  0
 10 33  1  0
 12 34  1  0
 12 35  1  0
 12 36  1  0
 13 37  1  0
 16 38  1  0
 18 39  1  0
 18 40  1  0
 18 41  1  0
 19 42  1  0
 19 43  1  0
 19 44  1  0
 20 45  1  0
 20 46  1  0
 21 47  1  0
 21 48  1  0
 22 49  1  0
 22 50  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
9,13-cis-Retinoate	Generator
3,7-Dimethyl-9-(2,6,6-trimethyl-1-cyclohexenyl)-(2E,4Z,6E,8Z)-nonatetraen-1-Oate	HMDB
3,7-Dimethyl-9-(2,6,6-trimethyl-1-cyclohexenyl)-(2E,4Z,6E,8Z)-nonatetraen-1-Oic acid	HMDB
9,13-cis-Retinoic acid	HMDB, Generator
9,13-cis-Retinoic acid anion	HMDB
9,13-cis-Vitamin-a-acid	HMDB
9,13-cis-Vitamin-alpha-acid	HMDB
9,13-Di-cis-ra	HMDB
9-cis,13-cis-Retinoate	HMDB
9-cis,13-cis-Retinoic acid	HMDB
DcVA	HMDB
9,13-Retinoic acid	MeSH, HMDB
9,13-Di-cis-retinoate	Generator

Chemical Formula

C₂₀H₂₈O₂

Average Molecular Weight

300.4351

Monoisotopic Molecular Weight

300.20893014

IUPAC Name

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

Traditional Name

9,13-di-cis-retinoic acid

CAS Registry Number

5352-74-9

SMILES

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

InChI Identifier

InChI=1S/C20H28O2/c1-15(8-6-9-16(2)14-19(21)22)11-12-18-17(3)10-7-13-20(18,4)5/h6,8-9,11-12,14H,7,10,13H2,1-5H3,(H,21,22)/b9-6+,12-11+,15-8-,16-14-

InChI Key

SHGAZHPCJJPHSC-CDMOMSTLSA-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

Retinoic acid
Diterpenoid
Retinoid skeleton
Medium-chain fatty acid
Branched fatty acid
Methyl-branched fatty acid
Fatty acyl
Unsaturated fatty acid
Fatty acid
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Hydrocarbon derivative
Organooxygen compound
Organic oxide
Organic oxygen compound
Carbonyl group
Aliphatic homomonocyclic compound

Molecular Framework

Aliphatic homomonocyclic compounds

External Descriptors

Retinoids (LMPR01090023 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cytoplasm (HMDB: HMDB0012874)
Cell membrane (HMDB: HMDB0012874)

Cellular substructure

Extracellular (HMDB: HMDB0012874)
Membrane (HMDB: HMDB0012874)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0012874)

Source

Endogenous

Endogenous (HMDB: HMDB0012874)

Animal

Animal (HMDB: HMDB0012874)

Exogenous

Food

Food (HMDB: HMDB0012874)

Process

Naturally occurring process

Biological process

Chemical reaction

Lipid peroxidation (HMDB: HMDB0012874)

Biochemical process

Fatty acid metabolism (HMDB: HMDB0012874)

Cellular process

Cell signaling (HMDB: HMDB0012874)

Biochemical pathway

Lipid metabolism pathway (HMDB: HMDB0012874)

Role

Biological role

Membrane stabilizer (HMDB: HMDB0012874)

Nutrient

Nutrient (HMDB: HMDB0012874)

Industrial application

Manufacturing industry

Material processing agent

Fluid processing agent

Surfactant

Surfactant (HMDB: HMDB0012874)

Emulsifier (HMDB: HMDB0012874)

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	181 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	6.30	HANSCH,C ET AL. (1995)

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	0.0048 g/L	ALOGPS
logP	5.66	ALOGPS
logP	5.01	ChemAxon
logS	-4.8	ALOGPS
pKa (Strongest Acidic)	5	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	37.3 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	97.79 m³·mol⁻¹	ChemAxon
Polarizability	35.87 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	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]+	178.172	31661259
DarkChem	[M-H]-	176.479	31661259
DeepCCS	[M+H]+	200.444	30932474
DeepCCS	[M-H]-	198.086	30932474
DeepCCS	[M-2H]-	231.701	30932474
DeepCCS	[M+Na]+	206.978	30932474
AllCCS	[M+H]+	177.6	32859911
AllCCS	[M+H-H2O]+	174.4	32859911
AllCCS	[M+NH4]+	180.5	32859911
AllCCS	[M+Na]+	181.4	32859911
AllCCS	[M-H]-	181.1	32859911
AllCCS	[M+Na-2H]-	181.7	32859911
AllCCS	[M+HCOO]-	182.5	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
9,13-cis-Retinoic acid	C\C(\C=C\C1=C(C)CCCC1(C)C)=C\C=C\C(\C)=C/C(O)=O	3735.6	Standard polar	33892256
9,13-cis-Retinoic acid	C\C(\C=C\C1=C(C)CCCC1(C)C)=C\C=C\C(\C)=C/C(O)=O	2481.2	Standard non polar	33892256
9,13-cis-Retinoic acid	C\C(\C=C\C1=C(C)CCCC1(C)C)=C\C=C\C(\C)=C/C(O)=O	2553.2	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
9,13-cis-Retinoic acid,1TMS,isomer #1	CC1=C(/C=C/C(C)=C\C=C\C(C)=C/C(=O)O[Si](C)(C)C)C(C)(C)CCC1	2701.4	Semi standard non polar	33892256
9,13-cis-Retinoic acid,1TBDMS,isomer #1	CC1=C(/C=C/C(C)=C\C=C\C(C)=C/C(=O)O[Si](C)(C)C(C)(C)C)C(C)(C)CCC1	2906.6	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 - 9,13-cis-Retinoic acid GC-MS (Non-derivatized) - 70eV, Positive	splash10-000i-2190000000-86aaab132a5b092ebf10	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 9,13-cis-Retinoic acid GC-MS (1 TMS) - 70eV, Positive	splash10-0a4i-5139000000-29caedb85908ca2b99f4	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 9,13-cis-Retinoic acid 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 - 9,13-cis-Retinoic acid 10V, Positive-QTOF	splash10-001i-0392000000-2208a551cdad109fbac3	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 9,13-cis-Retinoic acid 20V, Positive-QTOF	splash10-053i-1940000000-ace2a3043044e52c8ad3	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 9,13-cis-Retinoic acid 40V, Positive-QTOF	splash10-05nr-7900000000-1ee1af1ccb7ebac135f0	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 9,13-cis-Retinoic acid 10V, Negative-QTOF	splash10-052b-0090000000-ca9b2a996cc511290cb5	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 9,13-cis-Retinoic acid 20V, Negative-QTOF	splash10-0a5a-0090000000-4cb06190f795e5879208	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 9,13-cis-Retinoic acid 40V, Negative-QTOF	splash10-053i-3590000000-09c02aaba9f83079f9c2	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 9,13-cis-Retinoic acid 10V, Positive-QTOF	splash10-0zir-0973000000-3040e9e4a1a5448efbcb	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 9,13-cis-Retinoic acid 20V, Positive-QTOF	splash10-060c-1950000000-f3b9c9b378f60b8c49a9	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 9,13-cis-Retinoic acid 40V, Positive-QTOF	splash10-0ar3-5910000000-de22eb65f274483f3f98	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 9,13-cis-Retinoic acid 10V, Negative-QTOF	splash10-052b-0090000000-5f942e3b870e7bd0121b	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 9,13-cis-Retinoic acid 20V, Negative-QTOF	splash10-0a4i-0190000000-22b445382d3977280045	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 9,13-cis-Retinoic acid 40V, Negative-QTOF	splash10-016r-4900000000-0005b37f6d54a42a84f6	2021-09-24	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Extracellular
Membrane

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB029194

KNApSAcK ID

Not Available

Chemspider ID

4925342

KEGG Compound ID

C00777

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

6419708

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Simons K, Toomre D: Lipid rafts and signal transduction. Nat Rev Mol Cell Biol. 2000 Oct;1(1):31-9. [PubMed:11413487 ]
Watson AD: Thematic review series: systems biology approaches to metabolic and cardiovascular disorders. Lipidomics: a global approach to lipid analysis in biological systems. J Lipid Res. 2006 Oct;47(10):2101-11. Epub 2006 Aug 10. [PubMed:16902246 ]
Sethi JK, Vidal-Puig AJ: Thematic review series: adipocyte biology. Adipose tissue function and plasticity orchestrate nutritional adaptation. J Lipid Res. 2007 Jun;48(6):1253-62. Epub 2007 Mar 20. [PubMed:17374880 ]
Lingwood D, Simons K: Lipid rafts as a membrane-organizing principle. Science. 2010 Jan 1;327(5961):46-50. doi: 10.1126/science.1174621. [PubMed:20044567 ]
Gunstone, Frank D., John L. Harwood, and Albert J. Dijkstra (2007). The lipid handbook with CD-ROM. CRC Press.

Showing metabocard for 9,13-cis-Retinoic acid (HMDB0012874)

MOL for HMDB0012874 (9,13-cis-Retinoic acid)

3D MOL for HMDB0012874 (9,13-cis-Retinoic acid)

3D SDF for HMDB0012874 (9,13-cis-Retinoic acid)

3D-SDF for HMDB0012874 (9,13-cis-Retinoic acid)

PDB for HMDB0012874 (9,13-cis-Retinoic acid)

3D PDB for HMDB0012874 (9,13-cis-Retinoic acid)

SMILES for HMDB0012874 (9,13-cis-Retinoic acid)

INCHI for HMDB0012874 (9,13-cis-Retinoic acid)

Structure for HMDB0012874 (9,13-cis-Retinoic acid)

3D Structure for HMDB0012874 (9,13-cis-Retinoic acid)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra