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Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References enzymes (57)transporters (2) Show 59 proteins XML

enzymes (57)transporters (2) Show 59 proteins

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Record Information

Version

5.0

Status

Detected and Quantified

Creation Date

2006-02-16 11:10:57 UTC

Update Date

2022-03-07 02:49:10 UTC

HMDB ID

HMDB0001852

Secondary Accession Numbers

HMDB01852

Metabolite Identification

Common Name

all-trans-Retinoic acid

Description

all-trans-Retinoic acid is an isomer of retinoic acid, the oxidized form of vitamin A. Retinoic acid 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. As a drug, all-trans-retinoic acid is known as tretinoin. Tretinoin is derived from maternal vitamin A and is essential for normal growth and embryonic development. An excess of tretinoin can be teratogenic. Tretinoin 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).

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>
HMDB0001852

> <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-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 View Stereo Labels

Synonyms

Value	Source
(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 (ecl)	ChEBI
AGN 100335	ChEBI
all-(e)-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
beta-Retinoic acid	ChEBI
Eudyna	ChEBI
Renova	ChEBI
Retin-a	ChEBI
Retinoic acid	ChEBI
Retisol-a	ChEBI
Ro 1-5488	ChEBI
Solage	ChEBI
Stieva-a	ChEBI
trans-Retinoic acid	ChEBI
Tretin m	ChEBI
Tretinoin	ChEBI
Vesanoid	ChEBI
Vitamin a acid	ChEBI
Vitinoin	ChEBI
all-trans-Retinoate	Kegg
Avita	Kegg
Retin a	Kegg
(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 (ecl)	Generator
all-(e)-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
(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
Atralin	HMDB
Tretin-X	HMDB
all-trans-Retinoic acid	MeSH

Chemical Formula

C₂₀H₂₈O₂

Average Molecular Weight

300.442

Monoisotopic Molecular Weight

300.208930142

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

302-79-4

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

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 )

Ontology

Not Available

Adipose tissue (HMDB: HMDB0001852)

Epithelium

Epidermis (HMDB: HMDB0001852)

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 2756924)

Organ substructure

Adrenal cortex (HMDB: HMDB0001852)

Organ

Gland

Adrenal Gland (HMDB: HMDB0001852)

Cell

Fibroblasts (HMDB: HMDB0001852)
Neuron (HMDB: HMDB0001852)

Hematocyte

Platelet (HMDB: HMDB0001852)

Excreta

Biofluid or Excreta

Urine (PMID: 32966057)

Cellular substructure

Organelle

Endoplasmic reticulum (HMDB: HMDB0001852)
Nucleus (HMDB: HMDB0001852)

Source

Exogenous

Exogenous (HMDB: HMDB0001852)

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: HMDB0001852)

Process

Naturally occurring process

Biological process

Biochemical pathway

Metabolic pathway

Retinol Metabolism (HMDB: HMDB0001852)

Disease pathway

Vitamin A Deficiency (PathBank: SMP0120500)

Role

Physical Properties

State

Solid

Experimental Molecular Properties

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

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	0.0048 g/L	ALOGPS
logP	5.66	ALOGPS
logP	5.01	ChemAxon
logS	-4.8	ALOGPS
pKa (Strongest Acidic)	5	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	37.3 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	97.79 m³·mol⁻¹	ChemAxon
Polarizability	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

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
AllCCS	[M+H]+	178.029	32859911
AllCCS	[M-H]-	181.145	32859911
DeepCCS	[M+H]+	200.701	30932474
DeepCCS	[M-H]-	198.343	30932474
DeepCCS	[M-2H]-	231.939	30932474
DeepCCS	[M+Na]+	207.236	30932474
AllCCS	[M+H]+	178.0	32859911
AllCCS	[M+H-H2O]+	174.9	32859911
AllCCS	[M+NH4]+	180.9	32859911
AllCCS	[M+Na]+	181.8	32859911
AllCCS	[M-H]-	181.1	32859911
AllCCS	[M+Na-2H]-	181.7	32859911
AllCCS	[M+HCOO]-	182.5	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
all-trans-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
all-trans-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
all-trans-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
all-trans-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
all-trans-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 - all-trans-Retinoic acid GC-MS (Non-derivatized) - 70eV, Positive	splash10-000i-2090000000-db078f48efb8038384f2	2018-04-09	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - all-trans-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 - all-trans-Retinoic acid Quattro_QQQ 10V, Positive-QTOF (Annotated)	splash10-0udi-0009000000-12dbd83959268dee6dbf	2018-05-28	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - all-trans-Retinoic acid Quattro_QQQ 25V, Positive-QTOF (Annotated)	splash10-066r-4900000000-31c9262cbbf0bad5b738	2018-05-28	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - all-trans-Retinoic acid Quattro_QQQ 40V, Positive-QTOF (Annotated)	splash10-0fsl-9600000000-c6681587f0a9ae7a712e	2018-05-28	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - all-trans-Retinoic acid 20V, Positive-QTOF	splash10-0mc0-4941000000-401db468e6db7c5bbb5a	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - all-trans-Retinoic acid 35V, Negative-QTOF	splash10-0a4i-0090000000-d05c305f987a713dfaa0	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - all-trans-Retinoic acid 10V, Positive-QTOF	splash10-0udi-0239000000-09da873ecbe1e09a1602	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - all-trans-Retinoic acid 10V, Negative-QTOF	splash10-0002-0090000000-dca272cadb8a3ba3f819	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - all-trans-Retinoic acid 40V, Negative-QTOF	splash10-016r-9630000000-553ddaf9452713df67ee	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - all-trans-Retinoic acid 20V, Negative-QTOF	splash10-0a4i-0390000000-241af7f979164ecfbf34	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - all-trans-Retinoic acid 20V, Positive-QTOF	splash10-0mc0-4941000000-05bed4117d9ed953a2ca	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - all-trans-Retinoic acid 40V, Positive-QTOF	splash10-001i-9400000000-3ecfeb7f6c8384d2a0d3	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - all-trans-Retinoic acid 10V, Positive-QTOF	splash10-0udi-0239000000-2c6852256fcbebe1a2aa	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - all-trans-Retinoic acid 35V, Positive-QTOF	splash10-00di-0910000000-a1c1aa8b35e78558cd5b	2021-09-20	HMDB team, MONA	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - all-trans-Retinoic acid 10V, Positive-QTOF	splash10-0uei-0494000000-28e6366fdd47e8ba2117	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - all-trans-Retinoic acid 20V, Positive-QTOF	splash10-052r-2980000000-3e7fc78de83c23830416	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - all-trans-Retinoic acid 40V, Positive-QTOF	splash10-052r-5900000000-ef4d86f8bcf86959f794	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - all-trans-Retinoic acid 10V, Negative-QTOF	splash10-052b-0090000000-e07ffb4c1e5c63ab1b59	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - all-trans-Retinoic acid 20V, Negative-QTOF	splash10-052b-0090000000-a0a8411213bbd2543243	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - all-trans-Retinoic acid 40V, Negative-QTOF	splash10-000i-3690000000-97e6a74798dd69c30ad1	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - all-trans-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 - all-trans-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 - all-trans-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 - all-trans-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 - all-trans-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 - all-trans-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)	2018-05-28	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm
Extracellular
Membrane (predicted from logP)
Nucleus
Endoplasmic reticulum

Biospecimen Locations

Blood
Urine

Tissue Locations

Adipose Tissue
Adrenal Cortex
Adrenal Gland
Bladder
Brain
Epidermis
Fibroblasts
Intestine
Kidney
Liver
Lung
Neuron
Pancreas
Placenta
Platelet
Prostate
Spleen
Testis

Pathways

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

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected and Quantified	0.20 +/- 0.18 uM	Adult (>18 years old)	Female	Normal	Geigy Scientific ...	details
Blood	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	32966057	details
Blood	Detected and Quantified	0.0145 +/- 0.0092 uM	Adult (>18 years old)	Both	Normal	2756924	details
Urine	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	32966057	details

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB022710

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

Food Biomarker Ontology

Not Available

VMH ID

RETN

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Solladie, Guy; Girardin, Andre. Highly stereoselective synthesis of vitamin A and all-trans retinoic acid by low-valent titanium induced reductive elimination. Tetrahedron Letters (1988), 29(2), 213-16.

Material Safety Data Sheet (MSDS)

Not Available

General References

Czernik PJ, Little JM, Barone GW, Raufman JP, Radominska-Pandya A: Glucuronidation of estrogens and retinoic acid and expression of UDP-glucuronosyltransferase 2B7 in human intestinal mucosa. Drug Metab Dispos. 2000 Oct;28(10):1210-6. [PubMed:10997942 ]
Barua AB, Olson JA: Retinoyl beta-glucuronide: an endogenous compound of human blood. Am J Clin Nutr. 1986 Apr;43(4):481-5. [PubMed:3962900 ]
Napoli JL, Posch KP, Fiorella PD, Boerman MH: Physiological occurrence, biosynthesis and metabolism of retinoic acid: evidence for roles of cellular retinol-binding protein (CRBP) and cellular retinoic acid-binding protein (CRABP) in the pathway of retinoic acid homeostasis. Biomed Pharmacother. 1991;45(4-5):131-43. [PubMed:1932598 ]
Giannini G, Di Marcotullio L, Ristori E, Zani M, Crescenzi M, Scarpa S, Piaggio G, Vacca A, Peverali FA, Diana F, Screpanti I, Frati L, Gulino A: HMGI(Y) and HMGI-C genes are expressed in neuroblastoma cell lines and tumors and affect retinoic acid responsiveness. Cancer Res. 1999 May 15;59(10):2484-92. [PubMed:10344762 ]
Lee YF, Bao BY, Chang C: Modulation of the retinoic acid-induced cell apoptosis and differentiation by the human TR4 orphan nuclear receptor. Biochem Biophys Res Commun. 2004 Oct 22;323(3):876-83. [PubMed:15381082 ]
Mercader J, Ribot J, Murano I, Felipe F, Cinti S, Bonet ML, Palou A: Remodeling of white adipose tissue after retinoic acid administration in mice. Endocrinology. 2006 Nov;147(11):5325-32. Epub 2006 Jul 13. [PubMed:16840543 ]
Natsume N, Kondo S, Matsuyama Y, Sumida K, Inou H, Kawakami N, Sandell LJ, Iwata H: Analysis of cartilage-derived retinoic acid-sensitive protein in cerebrospinal fluid From patients With spinal diseases. Spine (Phila Pa 1976). 2001 Jan 15;26(2):157-60. [PubMed:11154535 ]
Baron JM, Heise R, Blaner WS, Neis M, Joussen S, Dreuw A, Marquardt Y, Saurat JH, Merk HF, Bickers DR, Jugert FK: Retinoic acid and its 4-oxo metabolites are functionally active in human skin cells in vitro. J Invest Dermatol. 2005 Jul;125(1):143-53. [PubMed:15982314 ]
Paez-Pereda M, Kovalovsky D, Hopfner U, Theodoropoulou M, Pagotto U, Uhl E, Losa M, Stalla J, Grubler Y, Missale C, Arzt E, Stalla GK: Retinoic acid prevents experimental Cushing syndrome. J Clin Invest. 2001 Oct;108(8):1123-31. [PubMed:11602619 ]
Saito S, Kondo S, Mishima S, Ishiguro N, Hasegawa Y, Sandell LJ, Iwata H: Analysis of cartilage-derived retinoic-acid-sensitive protein (CD-RAP) in synovial fluid from patients with osteoarthritis and rheumatoid arthritis. J Bone Joint Surg Br. 2002 Sep;84(7):1066-9. [PubMed:12358374 ]
Meyer E, Lambert WE, De Leenheer AP: Simultaneous determination of endogenous retinoic acid isomers and retinol in human plasma by isocratic normal-phase HPLC with ultraviolet detection. Clin Chem. 1994 Jan;40(1):48-57. [PubMed:8287543 ]
Masgrau-Peya E, Salomon D, Saurat JH, Meda P: In vivo modulation of connexins 43 and 26 of human epidermis by topical retinoic acid treatment. J Histochem Cytochem. 1997 Sep;45(9):1207-15. [PubMed:9283608 ]
Lopez-Boado YS, Klaus M, Dawson MI, Lopez-Otin C: Retinoic acid-induced expression of apolipoprotein D and concomitant growth arrest in human breast cancer cells are mediated through a retinoic acid receptor RARalpha-dependent signaling pathway. J Biol Chem. 1996 Dec 13;271(50):32105-11. [PubMed:8943263 ]
Stewart ME, Benoit AM, Downing DT, Strauss JS: Suppression of sebum secretion with 13-cis-retinoic acid: effect on individual skin surface lipids and implications for their anatomic origin. J Invest Dermatol. 1984 Jan;82(1):74-8. [PubMed:6228612 ]
Tse HK, Leung MB, Woolf AS, Menke AL, Hastie ND, Gosling JA, Pang CP, Shum AS: Implication of Wt1 in the pathogenesis of nephrogenic failure in a mouse model of retinoic acid-induced caudal regression syndrome. Am J Pathol. 2005 May;166(5):1295-307. [PubMed:15855632 ]
Patel JB, Huynh CK, Handratta VD, Gediya LK, Brodie AM, Goloubeva OG, Clement OO, Nanne IP, Soprano DR, Njar VC: Novel retinoic acid metabolism blocking agents endowed with multiple biological activities are efficient growth inhibitors of human breast and prostate cancer cells in vitro and a human breast tumor xenograft in nude mice. J Med Chem. 2004 Dec 30;47(27):6716-29. [PubMed:15615521 ]
Thiboutot D, Martin P, Volikos L, Gilliland K: Oxidative activity of the type 2 isozyme of 17beta-hydroxysteroid dehydrogenase (17beta-HSD) predominates in human sebaceous glands. J Invest Dermatol. 1998 Sep;111(3):390-5. [PubMed:9740229 ]
Holland LZ: Developmental biology: a chordate with a difference. Nature. 2007 May 10;447(7141):153-5. [PubMed:17495912 ]

Only showing the first 10 proteins. There are 59 proteins in total.

Show all enzymes and transporters

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 → all-trans-Retinoic acid + NADH + Hydrogen Ion	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 → all-trans-Retinoic acid + NADH + Hydrogen Ion	details

Enzyme Details

3. Cytochrome P450 4A11

General function:: Involved in monooxygenase activity
Specific function:: Catalyzes the omega- and (omega-1)-hydroxylation of various fatty acids such as laurate, myristate and palmitate. Has little activity toward prostaglandins A1 and E1. Oxidizes arachidonic acid to 20-hydroxyeicosatetraenoic acid (20-HETE).
Gene Name:: CYP4A11
Uniprot ID:: Q02928
Molecular weight:: 59347.31

Reactions

all-trans-Retinoic acid + NADPH + Hydrogen Ion + Oxygen → all-trans-18-Hydroxyretinoic acid + NADP + Water	details

Enzyme Details

4. UDP-glucuronosyltransferase 2B28

General function:: Involved in transferase activity, transferring hexosyl groups
Specific function:: UDPGTs are of major importance in the conjugation and subsequent elimination of potentially toxic xenobiotics and endogenous compounds. This isozyme has glucuronidating capacity with steroid substrates such as 5-beta-androstane 3-alpha,17-beta-diol, estradiol, ADT, eugenol and bile acids. Only isoform 1 seems to be active.
Gene Name:: UGT2B28
Uniprot ID:: Q9BY64
Molecular weight:: 38742.9

Reactions

all-trans-Retinoic acid + Uridine diphosphate glucuronic acid → Retinoyl b-glucuronide + Uridine 5'-diphosphate	details

Enzyme Details

5. UDP-glucuronosyltransferase 2B4

General function:: Involved in transferase activity, transferring hexosyl groups
Specific function:: UDPGTs are of major importance in the conjugation and subsequent elimination of potentially toxic xenobiotics and endogenous compounds. This isozyme is active on polyhydroxylated estrogens (such as estriol, 4-hydroxyestrone and 2-hydroxyestriol) and xenobiotics (such as 4-methylumbelliferone, 1-naphthol, 4-nitrophenol, 2-aminophenol, 4-hydroxybiphenyl and menthol). It is capable of 6 alpha-hydroxyglucuronidation of hyodeoxycholic acid.
Gene Name:: UGT2B4
Uniprot ID:: P06133
Molecular weight:: 60512.035

Reactions

all-trans-Retinoic acid + Uridine diphosphate glucuronic acid → Retinoyl b-glucuronide + Uridine 5'-diphosphate	details

Enzyme Details

6. UDP-glucuronosyltransferase 1-4

General function:: Involved in transferase activity, transferring hexosyl groups
Specific function:: UDPGT is of major importance in the conjugation and subsequent elimination of potentially toxic xenobiotics and endogenous compounds. This isoform glucuronidates bilirubin IX-alpha to form both the IX-alpha-C8 and IX-alpha-C12 monoconjugates and diconjugate.
Gene Name:: UGT1A4
Uniprot ID:: P22310
Molecular weight:: 60024.535

Reactions

all-trans-Retinoic acid + Uridine diphosphate glucuronic acid → Retinoyl b-glucuronide + Uridine 5'-diphosphate	details

Enzyme Details

7. UDP-glucuronosyltransferase 2B10

General function:: Involved in transferase activity, transferring hexosyl groups
Specific function:: UDPGT is of major importance in the conjugation and subsequent elimination of potentially toxic xenobiotics and endogenous compounds.
Gene Name:: UGT2B10
Uniprot ID:: P36537
Molecular weight:: 60773.485

Reactions

all-trans-Retinoic acid + Uridine diphosphate glucuronic acid → Retinoyl b-glucuronide + Uridine 5'-diphosphate	details

Enzyme Details

8. UDP-glucuronosyltransferase 2B7

General function:: Involved in transferase activity, transferring hexosyl groups
Specific function:: UDPGT is of major importance in the conjugation and subsequent elimination of potentially toxic xenobiotics and endogenous compounds. Its unique specificity for 3,4-catechol estrogens and estriol suggests it may play an important role in regulating the level and activity of these potent and active estrogen metabolites. Is also active with androsterone, hyodeoxycholic acid and tetrachlorocatechol (in vitro).
Gene Name:: UGT2B7
Uniprot ID:: P16662
Molecular weight:: 60720.15

Reactions

all-trans-Retinoic acid + Uridine diphosphate glucuronic acid → Retinoyl b-glucuronide + Uridine 5'-diphosphate	details

Enzyme Details

9. UDP-glucuronosyltransferase 2B15

General function:: Involved in transferase activity, transferring hexosyl groups
Specific function:: UDPGTs are of major importance in the conjugation and subsequent elimination of potentially toxic xenobiotics and endogenous compounds. This isozyme displays activity toward several classes of xenobiotic substrates, including simple phenolic compounds, 7-hydroxylated coumarins, flavonoids, anthraquinones, and certain drugs and their hydroxylated metabolites. It also catalyzes the glucuronidation of endogenous estrogens and androgens.
Gene Name:: UGT2B15
Uniprot ID:: P54855
Molecular weight:: 61035.815

Reactions

all-trans-Retinoic acid + Uridine diphosphate glucuronic acid → Retinoyl b-glucuronide + Uridine 5'-diphosphate	details

Enzyme Details

10. UDP-glucuronosyltransferase 2A1

General function:: Involved in transferase activity, transferring hexosyl groups
Specific function:: UDP-glucuronosyltransferases catalyze phase II biotransformation reactions in which lipophilic substrates are conjugated with glucuronic acid to increase water solubility and enhance excretion. They are of major importance in the conjugation and subsequent elimination of potentially toxic xenobiotics and endogenous compounds. Active on odorants and seems to be involved in olfaction; it could help clear lipophilic odorant molecules from the sensory epithelium.
Gene Name:: UGT2A1
Uniprot ID:: Q9Y4X1
Molecular weight:: 60771.605

Reactions

all-trans-Retinoic acid + Uridine diphosphate glucuronic acid → Retinoyl b-glucuronide + Uridine 5'-diphosphate	details

Transporters

Enzyme Details

1. Cellular retinoic acid-binding protein 1

General function:: Involved in binding
Specific function:: Cytosolic CRABPs may regulate the access of retinoic acid to the nuclear retinoic acid receptors
Gene Name:: CRABP1
Uniprot ID:: P29762
Molecular weight:: 15565.4

Enzyme Details

2. Cellular retinoic acid-binding protein 2

General function:: Involved in binding
Specific function:: Transports retinoic acid to the nucleus. Regulates the access of retinoic acid to the nuclear retinoic acid receptors
Gene Name:: CRABP2
Uniprot ID:: P29373
Molecular weight:: 15692.9

Only showing the first 10 proteins. There are 59 proteins in total.

Show all enzymes and transporters

Showing metabocard for all-trans-Retinoic acid (HMDB0001852)

MOL for HMDB0001852 (all-trans-Retinoic acid)

3D MOL for HMDB0001852 (all-trans-Retinoic acid)

3D SDF for HMDB0001852 (all-trans-Retinoic acid)

3D-SDF for HMDB0001852 (all-trans-Retinoic acid)

PDB for HMDB0001852 (all-trans-Retinoic acid)

3D PDB for HMDB0001852 (all-trans-Retinoic acid)

SMILES for HMDB0001852 (all-trans-Retinoic acid)

INCHI for HMDB0001852 (all-trans-Retinoic acid)

Structure for HMDB0001852 (all-trans-Retinoic acid)

3D Structure for HMDB0001852 (all-trans-Retinoic acid)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

Enzymes

Reactions

Reactions

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Reactions

Transporters