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Record Information

Version

5.0

Status

Detected and Quantified

Creation Date

2007-05-22 17:55:08 UTC

Update Date

2022-03-07 02:49:30 UTC

HMDB ID

HMDB0006219

Secondary Accession Numbers

HMDB06219

Metabolite Identification

Common Name

13-cis-Retinoic acid

Description

13-cis-Retinoic acid is a topical dermatologic agent that is used in the treatment of acne vulgaris and several other skin diseases. The drug has teratogenic and other adverse effects (PubChem). 13-cis-Retinoic acid is also a naturally occurring retinoid that is present in the circulation. Although 13-cis-retinoic acid (isotretinoin) does not have the potent gene regulatory activity of other isomers, it is an effective pharmacologic agent for treating a variety of dermatologic conditions (PMID:11606944 ). The steric conversion of 13-cis-retinoic acid (13-cRA) to all-trans-retinoic acid (t-RA) has been proposed as an activation mechanism for the observed therapeutic and teratogenic activities of 13-cRA (PMID:9806904 ). 13-cis Retinoic acid exerts its specific activity on human sebocytes through selective intracellular isomerization to all-trans retinoic acid and binding to retinoid acid receptors (PMID:10951254 ).

Structure

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

HMDB0006219
     RDKit          3D
13-cis-Retinoic acid
 50 50  0  0  0  0  0  0  0  0999 V2000
   -2.3258   -2.2848   -0.3377 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2272   -1.1114   -0.2271 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7200    0.0863   -0.0599 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3446    0.2654    0.0105 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1349    0.4231    0.0724 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0663   -0.3302   -0.0060 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0973   -1.7830   -0.3225 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2584    0.2851    0.1507 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4951   -0.4442    0.0812 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6599    0.2438    0.2463 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9053   -0.4541    0.1832 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9452   -1.9446   -0.0656 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0399    0.1806    0.3405 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1979    1.5890    0.5864 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.4084    2.0211    0.7126 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2214    2.5508    0.7064 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7295    1.2305    0.1105 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1108    2.5659   -0.0903 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3611    1.1702    1.4828 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8382    1.0416   -0.9000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5473   -0.2623   -0.6847 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6649   -1.3862   -0.3222 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9627   -2.4444   -1.3617 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5599   -2.3113    0.4294 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9642   -3.2002   -0.1311 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4202    1.4792   -0.7009 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0332    1.5230    0.4879 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2928   -1.9043   -1.1135 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0421   -2.0576   -0.8358 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8201   -2.4286    0.5186 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2266    1.3588    0.3285 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6386   -1.4903   -0.0782 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5689    1.2841    0.4170 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.9746   -2.2533   -0.2462 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5774   -2.4602    0.8510 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3337   -2.2251   -0.9331 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.9638   -0.4259    0.2800 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9643    3.1893   -0.0308 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2377    2.7926    0.5594 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8488    3.3879    0.1775 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8546    2.7844   -1.1434 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1602    2.1304    2.0434 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4666    1.0893    1.4560 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0077    0.2949    2.0801 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4635    1.0647   -1.9392 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5621    1.8682   -0.7223 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0910   -0.4634   -1.6408 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3404   -0.1762    0.1180 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9995   -1.8914    0.6170 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7876   -2.1671   -1.1544 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


  Mrv1652305261923522D          

 22 22  0  0  0  0            999 V2000
    0.0000    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
    0.7145    0.4125    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
    0.0000   -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
    6.4302    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0012    0.4125    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
    3.5724    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.8250    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
    5.7158    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125    1.5395    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125    1.5395    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
    1.4289   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7157   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1 16  1  0  0  0  0
  1 17  1  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  3 13  1  0  0  0  0
  4  3  2  0  0  0  0
 19  4  1  0  0  0  0
  5  4  1  0  0  0  0
  6  5  1  0  0  0  0
  2  6  1  0  0  0  0
  8  7  2  0  0  0  0
  9  8  1  0  0  0  0
 14  8  1  0  0  0  0
 10  9  2  0  0  0  0
 11 10  1  0  0  0  0
 12 11  2  0  0  0  0
 18 12  1  0  0  0  0
 15 12  1  0  0  0  0
 13 18  2  0  0  0  0
  7 20  1  0  0  0  0
 20 21  2  0  0  0  0
 20 22  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0006219

> <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-XFYACQKRSA-N

> <FORMULA>
C20H28O2

> <MOLECULAR_WEIGHT>
300.4351

> <EXACT_MASS>
300.20893014

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
50

> <JCHEM_AVERAGE_POLARIZABILITY>
36.151983823599814

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

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

> <JCHEM_VEBER_RULE>
1

$$$$

HMDB0006219
     RDKit          3D
13-cis-Retinoic acid
 50 50  0  0  0  0  0  0  0  0999 V2000
   -2.3258   -2.2848   -0.3377 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2272   -1.1114   -0.2271 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7200    0.0863   -0.0599 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3446    0.2654    0.0105 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1349    0.4231    0.0724 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0663   -0.3302   -0.0060 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0973   -1.7830   -0.3225 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2584    0.2851    0.1507 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4951   -0.4442    0.0812 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6599    0.2438    0.2463 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9053   -0.4541    0.1832 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9452   -1.9446   -0.0656 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0399    0.1806    0.3405 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1979    1.5890    0.5864 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.4084    2.0211    0.7126 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2214    2.5508    0.7064 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7295    1.2305    0.1105 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1108    2.5659   -0.0903 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3611    1.1702    1.4828 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8382    1.0416   -0.9000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5473   -0.2623   -0.6847 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6649   -1.3862   -0.3222 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9627   -2.4444   -1.3617 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5599   -2.3113    0.4294 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9642   -3.2002   -0.1311 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4202    1.4792   -0.7009 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0332    1.5230    0.4879 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2928   -1.9043   -1.1135 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0421   -2.0576   -0.8358 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8201   -2.4286    0.5186 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2266    1.3588    0.3285 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6386   -1.4903   -0.0782 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5689    1.2841    0.4170 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.9746   -2.2533   -0.2462 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5774   -2.4602    0.8510 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3337   -2.2251   -0.9331 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.9638   -0.4259    0.2800 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9643    3.1893   -0.0308 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2377    2.7926    0.5594 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8488    3.3879    0.1775 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8546    2.7844   -1.1434 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1602    2.1304    2.0434 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4666    1.0893    1.4560 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0077    0.2949    2.0801 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4635    1.0647   -1.9392 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5621    1.8682   -0.7223 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0910   -0.4634   -1.6408 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3404   -0.1762    0.1180 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9995   -1.8914    0.6170 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7876   -2.1671   -1.1544 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                                 26-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   26-MAY-19         0                                  
HETATM    1  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.334   0.770   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.334   0.770   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000  -1.540   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      12.003   0.770   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      10.669   1.540   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       9.336   0.770   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       6.668   0.770   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      10.669   3.080   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.335   3.080   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       0.770   2.874   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -0.770   2.874   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       4.001   0.770   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      12.003  -0.770   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      10.669  -1.540   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0      13.337  -1.540   0.000  0.00  0.00           O+0
CONECT    1   16   17    2    3                                             
CONECT    2    1    6                                                       
CONECT    3    1   13    4                                                  
CONECT    4    3   19    5                                                  
CONECT    5    4    6                                                       
CONECT    6    5    2                                                       
CONECT    7    8   20                                                       
CONECT    8    7    9   14                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   18   15                                                  
CONECT   13    3   18                                                       
CONECT   14    8                                                            
CONECT   15   12                                                            
CONECT   16    1                                                            
CONECT   17    1                                                            
CONECT   18   12   13                                                       
CONECT   19    4                                                            
CONECT   20    7   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20                                                            
MASTER        0    0    0    0    0    0    0    0   22    0   44    0
END

COMPND    HMDB0006219
HETATM    1  C1  UNL     1      -2.326  -2.285  -0.338  1.00  0.00           C  
HETATM    2  C2  UNL     1      -3.227  -1.111  -0.227  1.00  0.00           C  
HETATM    3  C3  UNL     1      -2.720   0.086  -0.060  1.00  0.00           C  
HETATM    4  C4  UNL     1      -1.345   0.265   0.010  1.00  0.00           C  
HETATM    5  C5  UNL     1      -0.135   0.423   0.072  1.00  0.00           C  
HETATM    6  C6  UNL     1       1.066  -0.330  -0.006  1.00  0.00           C  
HETATM    7  C7  UNL     1       1.097  -1.783  -0.323  1.00  0.00           C  
HETATM    8  C8  UNL     1       2.258   0.285   0.151  1.00  0.00           C  
HETATM    9  C9  UNL     1       3.495  -0.444   0.081  1.00  0.00           C  
HETATM   10  C10 UNL     1       4.660   0.244   0.246  1.00  0.00           C  
HETATM   11  C11 UNL     1       5.905  -0.454   0.183  1.00  0.00           C  
HETATM   12  C12 UNL     1       5.945  -1.945  -0.066  1.00  0.00           C  
HETATM   13  C13 UNL     1       7.040   0.181   0.340  1.00  0.00           C  
HETATM   14  C14 UNL     1       7.198   1.589   0.586  1.00  0.00           C  
HETATM   15  O1  UNL     1       8.408   2.021   0.713  1.00  0.00           O  
HETATM   16  O2  UNL     1       6.221   2.551   0.706  1.00  0.00           O  
HETATM   17  C15 UNL     1      -3.730   1.230   0.111  1.00  0.00           C  
HETATM   18  C16 UNL     1      -3.111   2.566  -0.090  1.00  0.00           C  
HETATM   19  C17 UNL     1      -4.361   1.170   1.483  1.00  0.00           C  
HETATM   20  C18 UNL     1      -4.838   1.042  -0.900  1.00  0.00           C  
HETATM   21  C19 UNL     1      -5.547  -0.262  -0.685  1.00  0.00           C  
HETATM   22  C20 UNL     1      -4.665  -1.386  -0.322  1.00  0.00           C  
HETATM   23  H1  UNL     1      -1.963  -2.444  -1.362  1.00  0.00           H  
HETATM   24  H2  UNL     1      -1.560  -2.311   0.429  1.00  0.00           H  
HETATM   25  H3  UNL     1      -2.964  -3.200  -0.131  1.00  0.00           H  
HETATM   26  H4  UNL     1      -1.420   1.479  -0.701  1.00  0.00           H  
HETATM   27  H5  UNL     1       0.033   1.523   0.488  1.00  0.00           H  
HETATM   28  H6  UNL     1       0.293  -1.904  -1.114  1.00  0.00           H  
HETATM   29  H7  UNL     1       2.042  -2.058  -0.836  1.00  0.00           H  
HETATM   30  H8  UNL     1       0.820  -2.429   0.519  1.00  0.00           H  
HETATM   31  H9  UNL     1       2.227   1.359   0.328  1.00  0.00           H  
HETATM   32  H10 UNL     1       3.639  -1.490  -0.078  1.00  0.00           H  
HETATM   33  H11 UNL     1       4.569   1.284   0.417  1.00  0.00           H  
HETATM   34  H12 UNL     1       6.975  -2.253  -0.246  1.00  0.00           H  
HETATM   35  H13 UNL     1       5.577  -2.460   0.851  1.00  0.00           H  
HETATM   36  H14 UNL     1       5.334  -2.225  -0.933  1.00  0.00           H  
HETATM   37  H15 UNL     1       7.964  -0.426   0.280  1.00  0.00           H  
HETATM   38  H16 UNL     1       5.964   3.189  -0.031  1.00  0.00           H  
HETATM   39  H17 UNL     1      -2.238   2.793   0.559  1.00  0.00           H  
HETATM   40  H18 UNL     1      -3.849   3.388   0.178  1.00  0.00           H  
HETATM   41  H19 UNL     1      -2.855   2.784  -1.143  1.00  0.00           H  
HETATM   42  H20 UNL     1      -4.160   2.130   2.043  1.00  0.00           H  
HETATM   43  H21 UNL     1      -5.467   1.089   1.456  1.00  0.00           H  
HETATM   44  H22 UNL     1      -4.008   0.295   2.080  1.00  0.00           H  
HETATM   45  H23 UNL     1      -4.464   1.065  -1.939  1.00  0.00           H  
HETATM   46  H24 UNL     1      -5.562   1.868  -0.722  1.00  0.00           H  
HETATM   47  H25 UNL     1      -6.091  -0.463  -1.641  1.00  0.00           H  
HETATM   48  H26 UNL     1      -6.340  -0.176   0.118  1.00  0.00           H  
HETATM   49  H27 UNL     1      -5.000  -1.891   0.617  1.00  0.00           H  
HETATM   50  H28 UNL     1      -4.788  -2.167  -1.154  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

HMDB0006219
     RDKit          3D
13-cis-Retinoic acid
 50 50  0  0  0  0  0  0  0  0999 V2000
   -2.3258   -2.2848   -0.3377 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2272   -1.1114   -0.2271 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7200    0.0863   -0.0599 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3446    0.2654    0.0105 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1349    0.4231    0.0724 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0663   -0.3302   -0.0060 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0973   -1.7830   -0.3225 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2584    0.2851    0.1507 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4951   -0.4442    0.0812 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6599    0.2438    0.2463 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9053   -0.4541    0.1832 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9452   -1.9446   -0.0656 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0399    0.1806    0.3405 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1979    1.5890    0.5864 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.4084    2.0211    0.7126 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2214    2.5508    0.7064 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7295    1.2305    0.1105 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1108    2.5659   -0.0903 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3611    1.1702    1.4828 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8382    1.0416   -0.9000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5473   -0.2623   -0.6847 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6649   -1.3862   -0.3222 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9627   -2.4444   -1.3617 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5599   -2.3113    0.4294 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9642   -3.2002   -0.1311 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4202    1.4792   -0.7009 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0332    1.5230    0.4879 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2928   -1.9043   -1.1135 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0421   -2.0576   -0.8358 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8201   -2.4286    0.5186 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2266    1.3588    0.3285 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6386   -1.4903   -0.0782 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5689    1.2841    0.4170 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.9746   -2.2533   -0.2462 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5774   -2.4602    0.8510 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3337   -2.2251   -0.9331 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.9638   -0.4259    0.2800 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9643    3.1893   -0.0308 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2377    2.7926    0.5594 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8488    3.3879    0.1775 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8546    2.7844   -1.1434 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1602    2.1304    2.0434 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4666    1.0893    1.4560 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0077    0.2949    2.0801 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4635    1.0647   -1.9392 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5621    1.8682   -0.7223 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0910   -0.4634   -1.6408 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3404   -0.1762    0.1180 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9995   -1.8914    0.6170 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7876   -2.1671   -1.1544 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
(7E,9E,11E,13Z)-Retinoic acid	ChEBI
13-cis-Vitamin a acid	ChEBI
13-RA	ChEBI
Accutane	ChEBI
Amnesteem	ChEBI
cis-RA	ChEBI
Claravis	ChEBI
Isotretinoina	ChEBI
Isotretinoine	ChEBI
Isotretinoino	ChEBI
Isotretinoinum	ChEBI
Neovitamin a acid	ChEBI
Absorica	Kegg
Sotret	Kegg
(7E,9E,11E,13Z)-Retinoate	Generator
13-cis-Retinoate	Generator
(13-cis)-Retinoate	HMDB
(13-cis)-Retinoic acid	HMDB
CIP-isotretinoin	HMDB
cis-Retinoate	HMDB
cis-Retinoic acid	HMDB
Isotretinoin	HMDB
Isotrex	HMDB
Retinoate	HMDB
Retinoic acid	HMDB
Roaccutan	HMDB
Roaccutane	HMDB
Roacutan	HMDB
Teriosal	HMDB
Isotretinoin zinc salt, 13 cis isomer	HMDB
Isotretinoin zinc salt, 13-cis-isomer	HMDB
13 cis Retinoic acid	HMDB
13-cis-Retinoate,isotretinoin	HMDB
13-cis-Retinoic acid	ChEBI

Chemical Formula

C₂₀H₂₈O₂

Average Molecular Weight

300.4351

Monoisotopic Molecular Weight

300.20893014

IUPAC Name

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

Traditional Name

isotretinoin

CAS Registry Number

4759-48-2

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-XFYACQKRSA-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

retinoic acid (CHEBI:6067 )
Retinoids (LMPR01090021 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 8699330)

Cellular substructure

Organelle

Endoplasmic reticulum (HMDB: HMDB0006219)
Nucleus (HMDB: HMDB0006219)

Source

Exogenous

Exogenous (HMDB: HMDB0006219)

Food

Animal origin

Poultry

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

Lagomorph

Ovis

Sheep (Mutton, Lamb) (FooDB: FOOD00473)

Bovine

Venison

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

Caprae

Domestic goat (FooDB: FOOD00529)

Swine

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

Equine

Horse (FooDB: FOOD00378)

Endogenous

Endogenous (HMDB: HMDB0006219)

Process

Not Available

Role

Not Available

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	0.0048 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	36.15 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]+	179.469	31661259
DarkChem	[M-H]-	178.352	31661259
DeepCCS	[M+H]+	199.545	30932474
DeepCCS	[M-H]-	197.187	30932474
DeepCCS	[M-2H]-	230.719	30932474
DeepCCS	[M+Na]+	205.981	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 Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.	8.33 minutes	32390414
Predicted by Siyang on May 30, 2022	25.9971 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	1.19 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	3405.6 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	798.4 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	300.1 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	502.7 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	379.8 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	1030.3 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	960.1 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	99.1 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	2162.1 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	747.4 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	1810.2 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	825.2 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	576.6 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	507.5 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	760.6 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	8.5 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
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
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
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
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
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 - 13-cis-Retinoic acid GC-MS (Non-derivatized) - 70eV, Positive	splash10-052r-2090000000-42b8aa0666b5a088671b	2017-08-28	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 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 - 13-cis-Retinoic acid GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 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
Experimental LC-MS/MS	LC-MS/MS Spectrum - 13-cis-Retinoic acid Quattro_QQQ 10V, Positive-QTOF (Annotated)	splash10-0udi-0009000000-12dbd83959268dee6dbf	2012-07-25	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 13-cis-Retinoic acid Quattro_QQQ 25V, Positive-QTOF (Annotated)	splash10-066r-4900000000-31c9262cbbf0bad5b738	2012-07-25	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 13-cis-Retinoic acid Quattro_QQQ 40V, Positive-QTOF (Annotated)	splash10-0fsl-9600000000-c6681587f0a9ae7a712e	2012-07-25	HMDB team, MONA	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 13-cis-Retinoic acid 10V, Positive-QTOF	splash10-0uei-0494000000-28e6366fdd47e8ba2117	2017-07-26	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 13-cis-Retinoic acid 20V, Positive-QTOF	splash10-052r-2980000000-3e7fc78de83c23830416	2017-07-26	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 13-cis-Retinoic acid 40V, Positive-QTOF	splash10-052r-5900000000-ef4d86f8bcf86959f794	2017-07-26	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 13-cis-Retinoic acid 10V, Negative-QTOF	splash10-052b-0090000000-e07ffb4c1e5c63ab1b59	2017-07-26	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 13-cis-Retinoic acid 20V, Negative-QTOF	splash10-052b-0090000000-a0a8411213bbd2543243	2017-07-26	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 13-cis-Retinoic acid 40V, Negative-QTOF	splash10-000i-3690000000-97e6a74798dd69c30ad1	2017-07-26	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 13-cis-Retinoic acid 10V, Positive-QTOF	splash10-0zir-0973000000-3040e9e4a1a5448efbcb	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 13-cis-Retinoic acid 20V, Positive-QTOF	splash10-060c-1950000000-f3b9c9b378f60b8c49a9	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 13-cis-Retinoic acid 40V, Positive-QTOF	splash10-0ar3-5910000000-de22eb65f274483f3f98	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 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 - 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 - 13-cis-Retinoic acid 40V, Negative-QTOF	splash10-016r-4900000000-0005b37f6d54a42a84f6	2021-09-24	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Experimental 2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, CDCl₃, experimental)	2012-12-05	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm
Extracellular
Membrane
Nucleus
Endoplasmic reticulum

Biospecimen Locations

Blood

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected and Quantified	0.003 +/- 0.001 uM	Adult (>18 years old)	Male	Normal	8699330	details
Blood	Detected and Quantified	0.003 +/- 0.0008 uM	Adult (>18 years old)	Female	Normal	8699330	details

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

DB00982

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB023843

KNApSAcK ID

Not Available

Chemspider ID

4445539

KEGG Compound ID

C07058

BioCyc ID

Not Available

BiGG ID

2430432

Wikipedia Link

Isotretinoin

METLIN ID

Not Available

PubChem Compound

5282379

PDB ID

Not Available

ChEBI ID

6067

Food Biomarker Ontology

Not Available

VMH ID

13_CIS_RETN

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Download (PDF)

General References

Blaner WS: Cellular metabolism and actions of 13-cis-retinoic acid. J Am Acad Dermatol. 2001 Nov;45(5):S129-35. [PubMed:11606944 ]
Chen H, Juchau MR: Recombinant human glutathione S-transferases catalyse enzymic isomerization of 13-cis-retinoic acid to all-trans-retinoic acid in vitro. Biochem J. 1998 Nov 15;336 ( Pt 1):223-6. [PubMed:9806904 ]
Tsukada M, Schroder M, Roos TC, Chandraratna RA, Reichert U, Merk HF, Orfanos CE, Zouboulis CC: 13-cis retinoic acid exerts its specific activity on human sebocytes through selective intracellular isomerization to all-trans retinoic acid and binding to retinoid acid receptors. J Invest Dermatol. 2000 Aug;115(2):321-7. [PubMed:10951254 ]

Enzymes

Enzyme Details

1. Retinal dehydrogenase 1

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

Reactions

Retinal + NAD + Water → 13-cis-Retinoic acid + NADH	details

Enzyme Details

2. Retinal dehydrogenase 2

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

Reactions

Retinal + NAD + Water → 13-cis-Retinoic acid + NADH	details

Showing metabocard for 13-cis-Retinoic acid (HMDB0006219)

MOL for HMDB0006219 (13-cis-Retinoic acid)

3D MOL for HMDB0006219 (13-cis-Retinoic acid)

3D SDF for HMDB0006219 (13-cis-Retinoic acid)

3D-SDF for HMDB0006219 (13-cis-Retinoic acid)

PDB for HMDB0006219 (13-cis-Retinoic acid)

3D PDB for HMDB0006219 (13-cis-Retinoic acid)

SMILES for HMDB0006219 (13-cis-Retinoic acid)

INCHI for HMDB0006219 (13-cis-Retinoic acid)

Structure for HMDB0006219 (13-cis-Retinoic acid)

3D Structure for HMDB0006219 (13-cis-Retinoic acid)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

Enzymes

Reactions

Reactions