NP-MRD: Showing NP-Card for Retinoic acid (NP0334089)

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Record Information

Version

2.0

Created at

2024-09-09 22:08:00 UTC

Updated at

2024-09-09 22:08:01 UTC

NP-MRD ID

NP0334089

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Retinoic acid

Description

Retinoic acid is the oxidized form of Vitamin A. It functions in determining position along embryonic anterior/posterior axis in chordates. It acts through Hox genes, which ultimately controls anterior/posterior patterning in early developmental stages (PMID: 17495912 ). It is an important regulator of gene expression during growth and development, and in neoplasms. Tretinoin, also known as retinoic acid and derived from maternal vitamin A, is essential for normal growth and embryonic development. An excess of tretinoin can be teratogenic. It is used in the treatment of psoriasis; acne vulgaris; and several other skin diseases. It has also been approved for use in promyelocytic leukemia (leukemia, promyelocytic, acute). [HMDB]

Structure

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

HMDB0001852
     RDKit          3D
all-trans-Retinoic acid
 50 50  0  0  0  0  0  0  0  0999 V2000
   -3.4071   -0.9003    2.7991 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8786   -0.5603    1.4353 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9920   -0.2909    0.5062 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5693   -0.3499    0.9242 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6056   -0.0890    0.1091 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8192   -0.1585    0.5561 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0633   -0.5390    1.9488 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7771    0.1155   -0.3009 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2056    0.0669    0.0730 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1242    0.3523   -0.8337 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5297    0.3230   -0.5326 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0620   -0.0197    0.7851 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3933    0.6216   -1.4953 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8253    0.6405   -1.3657 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.3945    0.3627   -0.2810 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.5878    0.9837   -2.5032 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3611    0.0206   -0.8698 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6660   -0.9241   -1.8630 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9053    1.4485   -1.1626 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8365   -0.1025   -1.1102 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6379    0.3975    0.0292 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3553   -0.5102    1.2325 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2253   -1.1774    3.4857 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7659   -1.8039    2.7012 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8548   -0.0435    3.2169 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2928   -0.6160    1.9400 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7367    0.2040   -0.9145 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5191    0.1920    2.5944 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5098   -1.5130    2.1261 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0829   -0.7137    2.2555 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5169    0.3857   -1.3133 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5170   -0.1921    1.0581 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7675    0.6226   -1.8619 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7662   -0.8943    0.7462 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6745    0.8391    1.1666 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3516   -0.2498    1.5722 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9688    0.8777   -2.4824 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.6232    1.9901   -2.6876 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1943   -0.3192   -2.6526 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0395   -1.6636   -1.3676 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4458   -1.5404   -2.4152 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3295    1.8614   -0.3369 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3592    1.4470   -2.1208 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8018    2.0998   -1.3374 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0428   -1.1947   -1.2164 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1085    0.4104   -2.0596 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7189    0.2973   -0.1807 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3923    1.4254    0.3307 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7974   -0.1021    2.1624 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7594   -1.5169    1.0122 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

      
  Mrv1652304202019462D          

 22 22  0  0  0  0            999 V2000
 9997.875010000.5889    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.589510000.1765    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.304010000.5889    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.019510000.1765    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.735110000.5889    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.450610000.1765    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10002.164110000.5889    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10002.879710000.1765    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10003.593210000.5889    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10004.308710000.1765    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10003.593210001.4138    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10002.164110001.4138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.304010001.4138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.4429 9998.5761    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.9730 9999.4954    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9996.447810001.4138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9996.446510000.5892    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9995.732010000.1767    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9995.7320 9999.3516    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9996.4465 9998.9392    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.1610 9999.3516    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.161010000.1767    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  3 13  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7 12  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  9 11  2  0  0  0  0
 17 18  1  0  0  0  0
 17 22  2  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 17 16  1  0  0  0  0
 21 15  1  0  0  0  0
 21 14  1  0  0  0  0
  1 22  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0334089

> <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-YCNIQYBTSA-N

> <FORMULA>
C20H28O2

> <MOLECULAR_WEIGHT>
300.442

> <EXACT_MASS>
300.208930142

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
50

> <JCHEM_AVERAGE_POLARIZABILITY>
36.845994315681

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2E,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>
97.79079999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
4.77e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
tretinoin

> <JCHEM_VEBER_RULE>
1

$$$$

HMDB0001852
     RDKit          3D
all-trans-Retinoic acid
 50 50  0  0  0  0  0  0  0  0999 V2000
   -3.4071   -0.9003    2.7991 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8786   -0.5603    1.4353 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9920   -0.2909    0.5062 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5693   -0.3499    0.9242 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6056   -0.0890    0.1091 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8192   -0.1585    0.5561 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0633   -0.5390    1.9488 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7771    0.1155   -0.3009 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2056    0.0669    0.0730 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1242    0.3523   -0.8337 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5297    0.3230   -0.5326 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0620   -0.0197    0.7851 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3933    0.6216   -1.4953 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8253    0.6405   -1.3657 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.3945    0.3627   -0.2810 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.5878    0.9837   -2.5032 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3611    0.0206   -0.8698 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6660   -0.9241   -1.8630 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9053    1.4485   -1.1626 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8365   -0.1025   -1.1102 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6379    0.3975    0.0292 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3553   -0.5102    1.2325 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2253   -1.1774    3.4857 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7659   -1.8039    2.7012 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8548   -0.0435    3.2169 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2928   -0.6160    1.9400 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7367    0.2040   -0.9145 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5191    0.1920    2.5944 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5098   -1.5130    2.1261 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0829   -0.7137    2.2555 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5169    0.3857   -1.3133 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5170   -0.1921    1.0581 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7675    0.6226   -1.8619 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7662   -0.8943    0.7462 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6745    0.8391    1.1666 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3516   -0.2498    1.5722 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9688    0.8777   -2.4824 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.6232    1.9901   -2.6876 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1943   -0.3192   -2.6526 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0395   -1.6636   -1.3676 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4458   -1.5404   -2.4152 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3295    1.8614   -0.3369 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3592    1.4470   -2.1208 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8018    2.0998   -1.3374 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0428   -1.1947   -1.2164 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1085    0.4104   -2.0596 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7189    0.2973   -0.1807 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3923    1.4254    0.3307 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7974   -0.1021    2.1624 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7594   -1.5169    1.0122 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                                 20-APR-20   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-APR-20         0                                  
HETATM    1  C   UNK     0    8662.7008667.766   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0    8664.0348666.996   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0    8665.3678667.766   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0    8666.7038666.996   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0    8668.0398667.766   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0    8669.3748666.996   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0    8670.7068667.766   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0    8672.0428666.996   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0    8673.3748667.766   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0    8674.7108666.996   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0    8673.3748669.306   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0    8670.7068669.306   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0    8665.3678669.306   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0    8661.8938664.009   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0    8662.8838665.725   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0    8660.0368669.306   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0    8660.0338667.767   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0    8658.7008666.997   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0    8658.7008665.456   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0    8660.0338664.687   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0    8661.3678665.456   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0    8661.3678666.997   0.000  0.00  0.00           C+0
CONECT    1    2   22                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4   13                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8   12                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9                                                            
CONECT   12    7                                                            
CONECT   13    3                                                            
CONECT   14   21                                                            
CONECT   15   21                                                            
CONECT   16   17                                                            
CONECT   17   18   22   16                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22   15   14                                             
CONECT   22   17   21    1                                                  
MASTER        0    0    0    0    0    0    0    0   22    0   44    0
END

COMPND    HMDB0001852
HETATM    1  C1  UNL     1      -3.407  -0.900   2.799  1.00  0.00           C  
HETATM    2  C2  UNL     1      -3.879  -0.560   1.435  1.00  0.00           C  
HETATM    3  C3  UNL     1      -2.992  -0.291   0.506  1.00  0.00           C  
HETATM    4  C4  UNL     1      -1.569  -0.350   0.924  1.00  0.00           C  
HETATM    5  C5  UNL     1      -0.606  -0.089   0.109  1.00  0.00           C  
HETATM    6  C6  UNL     1       0.819  -0.159   0.556  1.00  0.00           C  
HETATM    7  C7  UNL     1       1.063  -0.539   1.949  1.00  0.00           C  
HETATM    8  C8  UNL     1       1.777   0.115  -0.301  1.00  0.00           C  
HETATM    9  C9  UNL     1       3.206   0.067   0.073  1.00  0.00           C  
HETATM   10  C10 UNL     1       4.124   0.352  -0.834  1.00  0.00           C  
HETATM   11  C11 UNL     1       5.530   0.323  -0.533  1.00  0.00           C  
HETATM   12  C12 UNL     1       6.062  -0.020   0.785  1.00  0.00           C  
HETATM   13  C13 UNL     1       6.393   0.622  -1.495  1.00  0.00           C  
HETATM   14  C14 UNL     1       7.825   0.640  -1.366  1.00  0.00           C  
HETATM   15  O1  UNL     1       8.395   0.363  -0.281  1.00  0.00           O  
HETATM   16  O2  UNL     1       8.588   0.984  -2.503  1.00  0.00           O  
HETATM   17  C15 UNL     1      -3.361   0.021  -0.870  1.00  0.00           C  
HETATM   18  C16 UNL     1      -2.666  -0.924  -1.863  1.00  0.00           C  
HETATM   19  C17 UNL     1      -2.905   1.448  -1.163  1.00  0.00           C  
HETATM   20  C18 UNL     1      -4.836  -0.102  -1.110  1.00  0.00           C  
HETATM   21  C19 UNL     1      -5.638   0.398   0.029  1.00  0.00           C  
HETATM   22  C20 UNL     1      -5.355  -0.510   1.233  1.00  0.00           C  
HETATM   23  H1  UNL     1      -4.225  -1.177   3.486  1.00  0.00           H  
HETATM   24  H2  UNL     1      -2.766  -1.804   2.701  1.00  0.00           H  
HETATM   25  H3  UNL     1      -2.855  -0.043   3.217  1.00  0.00           H  
HETATM   26  H4  UNL     1      -1.293  -0.616   1.940  1.00  0.00           H  
HETATM   27  H5  UNL     1      -0.737   0.204  -0.914  1.00  0.00           H  
HETATM   28  H6  UNL     1       0.519   0.192   2.594  1.00  0.00           H  
HETATM   29  H7  UNL     1       0.510  -1.513   2.126  1.00  0.00           H  
HETATM   30  H8  UNL     1       2.083  -0.714   2.256  1.00  0.00           H  
HETATM   31  H9  UNL     1       1.517   0.386  -1.313  1.00  0.00           H  
HETATM   32  H10 UNL     1       3.517  -0.192   1.058  1.00  0.00           H  
HETATM   33  H11 UNL     1       3.767   0.623  -1.862  1.00  0.00           H  
HETATM   34  H12 UNL     1       6.766  -0.894   0.746  1.00  0.00           H  
HETATM   35  H13 UNL     1       6.674   0.839   1.167  1.00  0.00           H  
HETATM   36  H14 UNL     1       5.352  -0.250   1.572  1.00  0.00           H  
HETATM   37  H15 UNL     1       5.969   0.878  -2.482  1.00  0.00           H  
HETATM   38  H16 UNL     1       8.623   1.990  -2.688  1.00  0.00           H  
HETATM   39  H17 UNL     1      -2.194  -0.319  -2.653  1.00  0.00           H  
HETATM   40  H18 UNL     1      -2.040  -1.664  -1.368  1.00  0.00           H  
HETATM   41  H19 UNL     1      -3.446  -1.540  -2.415  1.00  0.00           H  
HETATM   42  H20 UNL     1      -2.330   1.861  -0.337  1.00  0.00           H  
HETATM   43  H21 UNL     1      -2.359   1.447  -2.121  1.00  0.00           H  
HETATM   44  H22 UNL     1      -3.802   2.100  -1.337  1.00  0.00           H  
HETATM   45  H23 UNL     1      -5.043  -1.195  -1.216  1.00  0.00           H  
HETATM   46  H24 UNL     1      -5.109   0.410  -2.060  1.00  0.00           H  
HETATM   47  H25 UNL     1      -6.719   0.297  -0.181  1.00  0.00           H  
HETATM   48  H26 UNL     1      -5.392   1.425   0.331  1.00  0.00           H  
HETATM   49  H27 UNL     1      -5.797  -0.102   2.162  1.00  0.00           H  
HETATM   50  H28 UNL     1      -5.759  -1.517   1.012  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

HMDB0001852
     RDKit          3D
all-trans-Retinoic acid
 50 50  0  0  0  0  0  0  0  0999 V2000
   -3.4071   -0.9003    2.7991 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8786   -0.5603    1.4353 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9920   -0.2909    0.5062 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5693   -0.3499    0.9242 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6056   -0.0890    0.1091 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8192   -0.1585    0.5561 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0633   -0.5390    1.9488 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7771    0.1155   -0.3009 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2056    0.0669    0.0730 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1242    0.3523   -0.8337 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5297    0.3230   -0.5326 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0620   -0.0197    0.7851 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3933    0.6216   -1.4953 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8253    0.6405   -1.3657 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.3945    0.3627   -0.2810 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.5878    0.9837   -2.5032 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3611    0.0206   -0.8698 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6660   -0.9241   -1.8630 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9053    1.4485   -1.1626 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8365   -0.1025   -1.1102 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6379    0.3975    0.0292 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3553   -0.5102    1.2325 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2253   -1.1774    3.4857 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7659   -1.8039    2.7012 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8548   -0.0435    3.2169 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2928   -0.6160    1.9400 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7367    0.2040   -0.9145 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5191    0.1920    2.5944 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5098   -1.5130    2.1261 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0829   -0.7137    2.2555 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5169    0.3857   -1.3133 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5170   -0.1921    1.0581 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7675    0.6226   -1.8619 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7662   -0.8943    0.7462 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6745    0.8391    1.1666 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3516   -0.2498    1.5722 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9688    0.8777   -2.4824 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.6232    1.9901   -2.6876 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1943   -0.3192   -2.6526 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0395   -1.6636   -1.3676 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4458   -1.5404   -2.4152 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3295    1.8614   -0.3369 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3592    1.4470   -2.1208 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8018    2.0998   -1.3374 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0428   -1.1947   -1.2164 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1085    0.4104   -2.0596 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7189    0.2973   -0.1807 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3923    1.4254    0.3307 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7974   -0.1021    2.1624 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7594   -1.5169    1.0122 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

Synonyms

Value	Source
(2E,4E,6E,8E)-3,7-Dimethyl-9-(2,6,6-trimethyl-1-cyclohexenyl)nona-2,4,6,8-tetraenoic acid	ChEBI
(all-e)-3,7-Dimethyl-9-(2,6,6-trimethyl-1-cyclohexen-1-yl)-2,4,6,8-nonatetraenoic acid	ChEBI
3,7-Dimethyl-9-(2,6,6-trimethyl-1-cyclohexene-1-yl)-2,4,6,8-nonatetraenoic acid	ChEBI
3,7-Dimethyl-9-(2,6,6-trimethylcyclohex-1-enyl)nona-2,4,6,8-all-trans-tetraenoic acid	ChEBI
3,7-Dimethyl-9-(2,6,6-trimethylcyclohexen-1-yl)nona-2E,4E,6E,8E-tetraenoic acid	ChEBI
AGN 100335	ChEBI
all-(e)-Retinoic acid	ChEBI
all-trans Retinoic acid	ChEBI
all-trans-beta-Retinoic acid	ChEBI
all-trans-Tretinoin	ChEBI
all-trans-Vitamin a acid	ChEBI
all-trans-Vitamin a1 acid	ChEBI
Altreno	ChEBI
Atralin	ChEBI
Avita	ChEBI
beta-Retinoic acid	ChEBI
Betarretin	ChEBI
Biacna	ChEBI
Cordes vas	ChEBI
Dermairol	ChEBI
Refissa	ChEBI
Renova	ChEBI
Retin-a	ChEBI
Retinoic acid	ChEBI
Retisol-a	ChEBI
Ro 1-5488	ChEBI
Stieva-a	ChEBI
trans-Retinoic acid	ChEBI
Tretin m	ChEBI
Tretinoin	ChEBI
Tretinoina	ChEBI
Tretinoine	ChEBI
Tretinoinum	ChEBI
Tri-luma	ChEBI
Veltin	ChEBI
Vesanoid	ChEBI
Vitamin a acid	ChEBI
Vitinoin	ChEBI
all-trans-Retinoate	Kegg
3,7-Dimethyl-9-(2,6,6-trimethyl-1-cyclohexene-1-yl)-2,4,6,8-nonatetraenoic acid (ecl)	Kegg
Retin a	Kegg
(2E,4E,6E,8E)-3,7-Dimethyl-9-(2,6,6-trimethyl-1-cyclohexenyl)nona-2,4,6,8-tetraenoate	Generator
(all-e)-3,7-Dimethyl-9-(2,6,6-trimethyl-1-cyclohexen-1-yl)-2,4,6,8-nonatetraenoate	Generator
3,7-Dimethyl-9-(2,6,6-trimethyl-1-cyclohexene-1-yl)-2,4,6,8-nonatetraenoate	Generator
3,7-Dimethyl-9-(2,6,6-trimethylcyclohex-1-enyl)nona-2,4,6,8-all-trans-tetraenoate	Generator
3,7-Dimethyl-9-(2,6,6-trimethylcyclohexen-1-yl)nona-2E,4E,6E,8E-tetraenoate	Generator
all-(e)-Retinoate	Generator
all-trans Retinoate	Generator
all-trans-b-Retinoate	Generator
all-trans-b-Retinoic acid	Generator
all-trans-beta-Retinoate	Generator
all-trans-Β-retinoate	Generator
all-trans-Β-retinoic acid	Generator
b-Retinoate	Generator
b-Retinoic acid	Generator
beta-Retinoate	Generator
Β-retinoate	Generator
Β-retinoic acid	Generator
Retinoate	Generator
trans-Retinoate	Generator
3,7-Dimethyl-9-(2,6,6-trimethyl-1-cyclohexene-1-yl)-2,4,6,8-nonatetraenoate (ecl)	Generator
Eudyna	HMDB
Solage	HMDB
(2E,4E,6E,8E)-3,7-Dimethyl-9-(2,6,6-trimethylcyclohexen-1-yl)nona-2,4,6,8-tetraenoate	HMDB
Tretinoin zinc salt	HMDB
trans Retinoic acid	HMDB
Acid, all-trans-retinoic	HMDB
Salt, tretinoin sodium	HMDB
beta all trans Retinoic acid	HMDB
beta-all-trans-Retinoic acid	HMDB
Acid, vitamin a	HMDB
Potassium salt, tretinoin	HMDB
Sodium salt, tretinoin	HMDB
Acid, beta-all-trans-retinoic	HMDB
Tretinoin potassium salt	HMDB
Zinc salt, tretinoin	HMDB
Acid, retinoic	HMDB
Acid, trans-retinoic	HMDB
Salt, tretinoin potassium	HMDB
Salt, tretinoin zinc	HMDB
Tretinoin sodium salt	HMDB
all trans Retinoic acid	HMDB
Retin-a micro	HMDB
Tretin-X	HMDB
all-trans-Retinoic acid	MeSH

Chemical Formula

C₂₀H₂₈O₂

Average Mass

300.4420 Da

Monoisotopic Mass

300.20893 Da

IUPAC Name

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

Traditional Name

tretinoin

CAS Registry Number

Not Available

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-YCNIQYBTSA-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

Not Available

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:15367 )
Retinoids (C00777 )
Retinoids (LMPR01090019 )

Physical Properties

State

Not Available

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
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	36.85 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

HMDB0001852

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB112204

KNApSAcK ID

Not Available

Chemspider ID

392618

KEGG Compound ID

C00777

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Tretinoin

METLIN ID

Not Available

PubChem Compound

444795

PDB ID

Not Available

ChEBI ID

15367

Good Scents ID

rw1216601

References

General References

Salekeen R, Siam MHB, Sharif DI, Lustgarten MS, Billah MM, Islam KMD: In silico insights into potential gut microbial modulation of NAD+ metabolism and longevity. J Biochem Mol Toxicol. 2021 Dec;35(12):e22925. doi: 10.1002/jbt.22925. Epub 2021 Sep 27. [PubMed:34580953 ]
Liu Y, Yu F, Dai S, Meng T, Zhu Y, Qiu G, Wen L, Zhou X, Yuan H, Hu F: All-Trans Retinoic Acid and Doxorubicin Delivery by Folic Acid Modified Polymeric Micelles for the Modulation of Pin1-Mediated DOX-Induced Breast Cancer Stemness and Metastasis. Mol Pharm. 2021 Nov 1;18(11):3966-3978. doi: 10.1021/acs.molpharmaceut.1c00220. Epub 2021 Sep 27. [PubMed:34579532 ]
Lu CH, Li KJ, Wu CH, Shen CY, Kuo YM, Hsieh SC, Yu CL: The FcgammaRIII Engagement Augments PMA-Stimulated Neutrophil Extracellular Traps (NETs) Formation by Granulocytes Partially via Cross-Talk between Syk-ERK-NF-kappaB and PKC-ROS Signaling Pathways. Biomedicines. 2021 Sep 1;9(9):1127. doi: 10.3390/biomedicines9091127. [PubMed:34572313 ]

Showing NP-Card for Retinoic acid (NP0334089)

MOL for NP0334089 (Retinoic acid)

3D MOL for NP0334089 (Retinoic acid)

3D SDF for NP0334089 (Retinoic acid)

3D-SDF for NP0334089 (Retinoic acid)

PDB for NP0334089 (Retinoic acid)

3D PDB for NP0334089 (Retinoic acid)

SMILES for NP0334089 (Retinoic acid)

INCHI for NP0334089 (Retinoic acid)

Structure for NP0334089 (Retinoic acid)

3D Structure for NP0334089 (Retinoic acid)