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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2007-05-22 17:55:08 UTC
Update Date2022-03-07 02:49:30 UTC
HMDB IDHMDB0006219
Secondary Accession Numbers
  • HMDB06219
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
Data?1582752375
Synonyms
ValueSource
(7E,9E,11E,13Z)-Retinoic acidChEBI
13-cis-Vitamin a acidChEBI
13-RAChEBI
AccutaneChEBI
AmnesteemChEBI
cis-RAChEBI
ClaravisChEBI
IsotretinoinaChEBI
IsotretinoineChEBI
IsotretinoinoChEBI
IsotretinoinumChEBI
Neovitamin a acidChEBI
AbsoricaKegg
SotretKegg
(7E,9E,11E,13Z)-RetinoateGenerator
13-cis-RetinoateGenerator
(13-cis)-RetinoateHMDB
(13-cis)-Retinoic acidHMDB
CIP-isotretinoinHMDB
cis-RetinoateHMDB
cis-Retinoic acidHMDB
IsotretinoinHMDB
IsotrexHMDB
RetinoateHMDB
Retinoic acidHMDB
RoaccutanHMDB
RoaccutaneHMDB
RoacutanHMDB
TeriosalHMDB
Isotretinoin zinc salt, 13 cis isomerHMDB
Isotretinoin zinc salt, 13-cis-isomerHMDB
13 cis Retinoic acidHMDB
13-cis-Retinoate,isotretinoinHMDB
13-cis-Retinoic acidChEBI
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 KeySHGAZHPCJJPHSC-XFYACQKRSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as retinoids. These are oxygenated derivatives of 3,7-dimethyl-1-(2,6,6-trimethylcyclohex-1-enyl)nona-1,3,5,7-tetraene and derivatives thereof.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassPrenol lipids
Sub ClassRetinoids
Direct ParentRetinoids
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 FrameworkAliphatic homomonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
ProcessNot Available
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.0048 g/LALOGPS
logP5.66ALOGPS
logP5.01ChemAxon
logS-4.8ALOGPS
pKa (Strongest Acidic)5ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area37.3 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity97.79 m³·mol⁻¹ChemAxon
Polarizability36.15 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveNoChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+179.46931661259
DarkChem[M-H]-178.35231661259
DeepCCS[M+H]+199.54530932474
DeepCCS[M-H]-197.18730932474
DeepCCS[M-2H]-230.71930932474
DeepCCS[M+Na]+205.98130932474
AllCCS[M+H]+177.632859911
AllCCS[M+H-H2O]+174.432859911
AllCCS[M+NH4]+180.532859911
AllCCS[M+Na]+181.432859911
AllCCS[M-H]-181.132859911
AllCCS[M+Na-2H]-181.732859911
AllCCS[M+HCOO]-182.532859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
13-cis-Retinoic acidC\C(\C=C\C1=C(C)CCCC1(C)C)=C/C=C/C(/C)=C\C(O)=O3735.6Standard polar33892256
13-cis-Retinoic acidC\C(\C=C\C1=C(C)CCCC1(C)C)=C/C=C/C(/C)=C\C(O)=O2481.2Standard non polar33892256
13-cis-Retinoic acidC\C(\C=C\C1=C(C)CCCC1(C)C)=C/C=C/C(/C)=C\C(O)=O2553.2Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
13-cis-Retinoic acid,1TMS,isomer #1CC1=C(/C=C/C(C)=C/C=C/C(C)=C\C(=O)O[Si](C)(C)C)C(C)(C)CCC12701.4Semi standard non polar33892256
13-cis-Retinoic acid,1TBDMS,isomer #1CC1=C(/C=C/C(C)=C/C=C/C(C)=C\C(=O)O[Si](C)(C)C(C)(C)C)C(C)(C)CCC12906.6Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 13-cis-Retinoic acid GC-MS (Non-derivatized) - 70eV, Positivesplash10-052r-2090000000-42b8aa0666b5a088671b2017-08-28Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 13-cis-Retinoic acid GC-MS (1 TMS) - 70eV, Positivesplash10-0a4i-5139000000-29caedb85908ca2b99f42017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 13-cis-Retinoic acid GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 13-cis-Retinoic acid GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental LC-MS/MSLC-MS/MS Spectrum - 13-cis-Retinoic acid Quattro_QQQ 10V, Positive-QTOF (Annotated)splash10-0udi-0009000000-12dbd83959268dee6dbf2012-07-25HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - 13-cis-Retinoic acid Quattro_QQQ 25V, Positive-QTOF (Annotated)splash10-066r-4900000000-31c9262cbbf0bad5b7382012-07-25HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - 13-cis-Retinoic acid Quattro_QQQ 40V, Positive-QTOF (Annotated)splash10-0fsl-9600000000-c6681587f0a9ae7a712e2012-07-25HMDB team, MONAView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 13-cis-Retinoic acid 10V, Positive-QTOFsplash10-0uei-0494000000-28e6366fdd47e8ba21172017-07-26Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 13-cis-Retinoic acid 20V, Positive-QTOFsplash10-052r-2980000000-3e7fc78de83c238304162017-07-26Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 13-cis-Retinoic acid 40V, Positive-QTOFsplash10-052r-5900000000-ef4d86f8bcf86959f7942017-07-26Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 13-cis-Retinoic acid 10V, Negative-QTOFsplash10-052b-0090000000-e07ffb4c1e5c63ab1b592017-07-26Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 13-cis-Retinoic acid 20V, Negative-QTOFsplash10-052b-0090000000-a0a8411213bbd25432432017-07-26Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 13-cis-Retinoic acid 40V, Negative-QTOFsplash10-000i-3690000000-97e6a74798dd69c30ad12017-07-26Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 13-cis-Retinoic acid 10V, Positive-QTOFsplash10-0zir-0973000000-3040e9e4a1a5448efbcb2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 13-cis-Retinoic acid 20V, Positive-QTOFsplash10-060c-1950000000-f3b9c9b378f60b8c49a92021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 13-cis-Retinoic acid 40V, Positive-QTOFsplash10-0ar3-5910000000-de22eb65f274483f3f982021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 13-cis-Retinoic acid 10V, Negative-QTOFsplash10-052b-0090000000-5f942e3b870e7bd0121b2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 13-cis-Retinoic acid 20V, Negative-QTOFsplash10-0a4i-0190000000-22b445382d39772800452021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 13-cis-Retinoic acid 40V, Negative-QTOFsplash10-016r-4900000000-0005b37f6d54a42a84f62021-09-24Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Experimental 2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, CDCl3, experimental)2012-12-05Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
  • Membrane
  • Nucleus
  • Endoplasmic reticulum
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
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 IDDB00982
Phenol Explorer Compound IDNot Available
FooDB IDFDB023843
KNApSAcK IDNot Available
Chemspider ID4445539
KEGG Compound IDC07058
BioCyc IDNot Available
BiGG ID2430432
Wikipedia LinkIsotretinoin
METLIN IDNot Available
PubChem Compound5282379
PDB IDNot Available
ChEBI ID6067
Food Biomarker OntologyNot Available
VMH ID13_CIS_RETN
MarkerDB IDNot Available
Good Scents IDNot Available
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. [PubMed: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. [PubMed: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. [PubMed: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