NP-MRD: Showing NP-Card for 13-cis-Retinoic acid (NP0000960)

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Record Information

Version

2.0

Created at

2007-05-22 17:55:08 UTC

Updated at

2024-09-17 15:43:34 UTC

NP-MRD ID

NP0000960

Secondary Accession Numbers

None

Natural Product 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>
NP0000960

> <DATABASE_NAME>
NP-MRD

> <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 NMR Assignments

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 Mass

300.4351 Da

Monoisotopic Mass

300.20893 Da

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

Experimental Spectra

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

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

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

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as retinoids. These are oxygenated derivatives of 3,7-dimethyl-1-(2,6,6-trimethylcyclohex-1-enyl)nona-1,3,5,7-tetraene and derivatives thereof.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Retinoids

Direct Parent

Retinoids

Alternative Parents

Substituents

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 )

Physical Properties

State

Solid

Experimental Properties

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

Predicted Properties

Property	Value	Source
Water Solubility	0.0048 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

External Links

HMDB ID

HMDB0006219

DrugBank ID

DB00982

Phenol Explorer Compound ID

Not Available

FoodDB 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

Good Scents ID

Not Available

References

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 ]
Ellis CN, Krach KJ: Uses and complications of isotretinoin therapy. J Am Acad Dermatol. 2001 Nov;45(5):S150-7. doi: 10.1067/mjd.2001.113717. [PubMed:11606947 ]
Niles RM: The use of retinoids in the prevention and treatment of skin cancer. Expert Opin Pharmacother. 2002 Mar;3(3):299-303. doi: 10.1517/14656566.3.3.299. [PubMed:11866680 ]

Showing NP-Card for 13-cis-Retinoic acid (NP0000960)

MOL for NP0000960 (13-cis-Retinoic acid)

3D MOL for NP0000960 (13-cis-Retinoic acid)

3D SDF for NP0000960 (13-cis-Retinoic acid)

3D-SDF for NP0000960 (13-cis-Retinoic acid)

PDB for NP0000960 (13-cis-Retinoic acid)

3D PDB for NP0000960 (13-cis-Retinoic acid)

SMILES for NP0000960 (13-cis-Retinoic acid)

INCHI for NP0000960 (13-cis-Retinoic acid)

Structure for NP0000960 (13-cis-Retinoic acid)

3D Structure for NP0000960 (13-cis-Retinoic acid)