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Record Information
Version3.6
Creation Date2007-05-22 17:55:08 UTC
Update Date2016-02-11 01:07:25 UTC
HMDB IDHMDB06219
Secondary Accession NumbersNone
Metabolite Identification
Common Name13-cis-Retinoic acid
Description13-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
Thumb
Synonyms
ValueSource
(7E,9E,11E,13Z)-Retinoic acidChEBI
13-cis-Retinoic acidChEBI
13-cis-Vitamin a acidChEBI
13-RAChEBI
AccutaneChEBI
AmnesteemChEBI
cis-RAChEBI
ClaravisChEBI
IsotretinoinaChEBI
IsotretinoineChEBI
IsotretinoinoChEBI
IsotretinoinumChEBI
Neovitamin a acidChEBI
(7E,9E,11E,13Z)-RetinoateGenerator
13-cis-RetinoateGenerator
(13-cis)-RetinoateHMDB
(13-cis)-Retinoic acidHMDB
CIP-isotretinoinHMDB
cis-RetinoateHMDB
cis-Retinoic acidHMDB
IsotrexHMDB
RetinoateHMDB
Retinoic acidHMDB
RoaccutanHMDB
RoaccutaneHMDB
RoacutanHMDB
SotretHMDB
TeriosalHMDB
Chemical FormulaC20H28O2
Average Molecular Weight300.4351
Monoisotopic Molecular Weight300.20893014
IUPAC Name(2Z,4E,6E,8E)-3,7-dimethyl-9-(2,6,6-trimethylcyclohex-1-en-1-yl)nona-2,4,6,8-tetraenoic acid
Traditional Nameisotretinoin
CAS Registry Number4759-48-2
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 KeyInChIKey=SHGAZHPCJJPHSC-XFYACQKRSA-N
Chemical Taxonomy
DescriptionThis compound 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.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassPrenol lipids
Sub ClassRetinoids
Direct ParentRetinoids
Alternative Parents
Substituents
  • Retinoid skeleton
  • Diterpenoid
  • Carbocyclic fatty acid
  • Medium-chain fatty acid
  • Methyl-branched fatty acid
  • Branched fatty acid
  • Fatty acyl
  • Fatty acid
  • Unsaturated fatty acid
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Carboxylic acid derivative
  • Hydrocarbon derivative
  • Organooxygen compound
  • Carbonyl group
  • Aliphatic homomonocyclic compound
Molecular FrameworkAliphatic homomonocyclic compounds
External Descriptors
Ontology
StatusDetected and Quantified
Origin
  • Endogenous
  • Food
Biofunction
  • Cell signaling
  • Fuel and energy storage
  • Fuel or energy source
  • Membrane integrity/stability
Application
  • Nutrients
  • Stabilizers
  • Surfactants and Emulsifiers
Cellular locations
  • Cytoplasm
  • Extracellular
  • Membrane
  • Nucleus
  • Endoplasmic reticulum
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility0.0048 mg/mLALOGPS
logP5.66ALOGPS
logP5.01ChemAxon
logS-4.8ALOGPS
pKa (Strongest Acidic)5ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area37.3 Å2ChemAxon
Rotatable Bond Count5ChemAxon
Refractivity97.79 m3·mol-1ChemAxon
Polarizability36.15 Å3ChemAxon
Number of Rings1ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash Key
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-0udi-0009000000-12dbd83959268dee6dbfView in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-066r-4900000000-31c9262cbbf0bad5b738View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-0fsl-9600000000-c6681587f0a9ae7a712eView in MoNA
1D NMR1H NMR SpectrumNot Available
2D NMR[1H,13C] 2D NMR SpectrumNot Available
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
  • Membrane
  • Nucleus
  • Endoplasmic reticulum
Biofluid Locations
  • Blood
Tissue LocationNot Available
PathwaysNot Available
Normal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified0.003 +/- 0.001 uMAdult (>18 years old)MaleNormal details
BloodDetected and Quantified0.003 +/- 0.0008 uMAdult (>18 years old)FemaleNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
DrugBank Metabolite IDNot Available
Phenol Explorer Compound IDNot Available
Phenol Explorer Metabolite IDNot Available
FoodDB IDFDB023843
KNApSAcK IDNot Available
Chemspider ID4445539
KEGG Compound IDD00348
BioCyc IDNot Available
BiGG ID2430432
Wikipedia LinkNot Available
NuGOwiki LinkHMDB06219
Metagene LinkHMDB06219
METLIN IDNot Available
PubChem Compound5282379
PDB IDNot Available
ChEBI ID6067
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. Blaner WS: Cellular metabolism and actions of 13-cis-retinoic acid. J Am Acad Dermatol. 2001 Nov;45(5):S129-35. [11606944 ]
  2. 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. [9806904 ]
  3. 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. [10951254 ]

Enzymes

General function:
Involved in oxidoreductase activity
Specific function:
Binds free retinal and cellular retinol-binding protein-bound retinal. Can convert/oxidize retinaldehyde to retinoic acid (By similarity).
Gene Name:
ALDH1A1
Uniprot ID:
P00352
Molecular weight:
54861.44
Reactions
Retinal + NAD + Water → 13-cis-Retinoic acid + NADHdetails
General function:
Involved in oxidoreductase activity
Specific function:
Recognizes as substrates free retinal and cellular retinol-binding protein-bound retinal. Does metabolize octanal and decanal but does not metabolize citral, benzaldehyde, acetaldehyde and propanal efficiently (By similarity).
Gene Name:
ALDH1A2
Uniprot ID:
O94788
Molecular weight:
54672.24
Reactions
Retinal + NAD + Water → 13-cis-Retinoic acid + NADHdetails