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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2006-05-22 14:17:50 UTC
Update Date2022-03-07 02:49:15 UTC
HMDB IDHMDB0002369
Secondary Accession Numbers
  • HMDB02369
Metabolite Identification
Common Name9-cis-Retinoic acid
Description9-cis-Retinoic acid is an active retinoid that regulates expression of retinoid responsive genes, serving as a ligand for two classes of ligand-dependent transcription factors: the retinoic acid receptors and retinoid X receptors. Retinoids (vitamin A and its analogs) are essential dietary substances that are needed by mammals for reproduction, normal embryogenesis, growth, vision, and maintaining normal cellular differentiation and the integrity of the immune system. Within cells, retinoids regulate gene transcription acting through ligand-dependent transcription factors, the retinoic acid receptors (RARs), and the retinoid X receptors (RXRs). all-trans-Retinoic acid binds only to RARs with high affinity, whereas its 9-cis isomer binds with high affinity to both RARs and RXRs. The actions of all-trans- and 9-cis-retinoic acid in regulating cellular responses are distinct and not interchangeable (PMID: 9115228 ).
Structure
Data?1582752246
Synonyms
ValueSource
(2E,4E,6Z,8E)-3,7-Dimethyl-9-(2,6,6-trimethyl-1-cyclohexen-1-yl)-2,4,6,8-nonatetraenoic acidChEBI
(7E,9Z,11E,13E)-Retinoic acidChEBI
9(Z)-Retinoic acidChEBI
9-cis-TretinoinChEBI
AlitretinoinChEBI
AlitretinoinaChEBI
AlitretinoineChEBI
AlitretinoinumChEBI
PanretinChEBI
PanretynChEBI
(2E,4E,6Z,8E)-3,7-Dimethyl-9-(2,6,6-trimethyl-1-cyclohexen-1-yl)-2,4,6,8-nonatetraenoateGenerator
(7E,9Z,11E,13E)-RetinoateGenerator
9(Z)-RetinoateGenerator
9-cis-RetinoateGenerator
9 cis Retinoic acidMeSH
9CRA compoundMeSH
ToctinoMeSH
15-apo-beta-Caroten-15-OateHMDB
15-apo-beta-Caroten-15-Oic acidHMDB
9-RetinoateHMDB
9-Retinoic acidHMDB
AberelHMDB
AberelaHMDB
AirolHMDB
AknotenHMDB
all-trans- Vitamin a1 acidHMDB
all-trans-b-RetinoateHMDB
all-trans-b-Retinoic acidHMDB
all-trans-beta-RetinoateHMDB
all-trans-beta-Retinoic acidHMDB
all-trans-Vitamin a acidHMDB
alpha-VitaminsyreHMDB
AtragenHMDB
AvitaHMDB
AvitoinHMDB
b-RetinoateHMDB
b-Retinoic acidHMDB
beta-RetinoateHMDB
beta-Retinoic acidHMDB
DermairolHMDB
EffedermHMDB
Epi-aberelHMDB
EudynaHMDB
Isotretinoin retinoateHMDB
Isotretinoin retinoic acidHMDB
Panretin gelHMDB
PanrexinHMDB
RenovaHMDB
RetacnylHMDB
Retin aHMDB
Retin-aHMDB
Retin-a microHMDB
RetinoateHMDB
Retinoic acidHMDB
RetinovaHMDB
trans-RetinoateHMDB
trans-Retinoic acidHMDB
trans-Vitamin a acidHMDB
TretinoinHMDB
Tretinoin/all-trans retinoateHMDB
Tretinoin/all-trans retinoic acidHMDB
TretinonHMDB
VesanoidHMDB
VesnaroidHMDB
Chemical FormulaC20H28O2
Average Molecular Weight300.4351
Monoisotopic Molecular Weight300.20893014
IUPAC Name(2E,4E,6Z,8E)-3,7-dimethyl-9-(2,6,6-trimethylcyclohex-1-en-1-yl)nona-2,4,6,8-tetraenoic acid
Traditional Namealitretinoin
CAS Registry Number5300-03-8
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-ZVCIMWCZSA-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
Process
Role
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct TypeData SourceCCS Value (Å2)Reference
[M-H]-MetCCS_train_neg200.00630932474
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
Polarizability35.89 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]+178.1731661259
DarkChem[M-H]-177.23731661259
DeepCCS[M+H]+199.60530932474
DeepCCS[M-H]-197.24730932474
DeepCCS[M-2H]-230.78530932474
DeepCCS[M+Na]+206.01230932474
AllCCS[M+H]+178.032859911
AllCCS[M+H-H2O]+174.932859911
AllCCS[M+NH4]+180.932859911
AllCCS[M+Na]+181.832859911
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
9-cis-Retinoic acidC\C(\C=C\C1=C(C)CCCC1(C)C)=C\C=C\C(\C)=C\C(O)=O3735.6Standard polar33892256
9-cis-Retinoic acidC\C(\C=C\C1=C(C)CCCC1(C)C)=C\C=C\C(\C)=C\C(O)=O2481.2Standard non polar33892256
9-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
9-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
9-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 - 9-cis-Retinoic acid GC-MS (Non-derivatized) - 70eV, Positivesplash10-000i-2190000000-86aaab132a5b092ebf102017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 9-cis-Retinoic acid GC-MS (1 TMS) - 70eV, Positivesplash10-0a4i-5139000000-29caedb85908ca2b99f42017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 9-cis-Retinoic acid GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 9-cis-Retinoic acid 10V, Positive-QTOFsplash10-0uei-0494000000-28e6366fdd47e8ba21172016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 9-cis-Retinoic acid 20V, Positive-QTOFsplash10-052r-2980000000-3e7fc78de83c238304162016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 9-cis-Retinoic acid 40V, Positive-QTOFsplash10-052r-5900000000-ef4d86f8bcf86959f7942016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 9-cis-Retinoic acid 10V, Negative-QTOFsplash10-052b-0090000000-e07ffb4c1e5c63ab1b592016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 9-cis-Retinoic acid 20V, Negative-QTOFsplash10-052b-0090000000-a0a8411213bbd25432432016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 9-cis-Retinoic acid 40V, Negative-QTOFsplash10-000i-3690000000-97e6a74798dd69c30ad12016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 9-cis-Retinoic acid 10V, Negative-QTOFsplash10-052b-0090000000-5f942e3b870e7bd0121b2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 9-cis-Retinoic acid 20V, Negative-QTOFsplash10-0a4i-0190000000-22b445382d39772800452021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 9-cis-Retinoic acid 40V, Negative-QTOFsplash10-016r-4900000000-0005b37f6d54a42a84f62021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 9-cis-Retinoic acid 10V, Positive-QTOFsplash10-0zir-0973000000-3040e9e4a1a5448efbcb2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 9-cis-Retinoic acid 20V, Positive-QTOFsplash10-060c-1950000000-f3b9c9b378f60b8c49a92021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 9-cis-Retinoic acid 40V, Positive-QTOFsplash10-0ar3-5910000000-de22eb65f274483f3f982021-09-22Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Extracellular
  • Membrane
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified0.0042 +/-0.001 uMAdult (>18 years old)MaleNormal details
BloodDetected and Quantified0.0056 +/- 0.002 uMAdult (>18 years old)FemaleNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB00523
Phenol Explorer Compound IDNot Available
FooDB IDFDB001084
KNApSAcK IDNot Available
Chemspider ID395778
KEGG Compound IDC15493
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkAlitretinoin
METLIN IDNot Available
PubChem Compound449171
PDB IDNot Available
ChEBI ID50648
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Mertz JR, Shang E, Piantedosi R, Wei S, Wolgemuth DJ, Blaner WS: Identification and characterization of a stereospecific human enzyme that catalyzes 9-cis-retinol oxidation. A possible role in 9-cis-retinoic acid formation. J Biol Chem. 1997 May 2;272(18):11744-9. [PubMed:9115228 ]

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
9-cis-Retinal + NAD + Water → 9-cis-Retinoic acid + NADH + Hydrogen Iondetails
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
9-cis-Retinal + NAD + Water → 9-cis-Retinoic acid + NADH + Hydrogen Iondetails
General function:
Involved in sequence-specific DNA binding transcription factor activity
Specific function:
Nuclear hormone receptor. Involved in the retinoic acid response pathway. Binds 9-cis retinoic acid (9C-RA)
Gene Name:
RXRB
Uniprot ID:
P28702
Molecular weight:
56921.4
General function:
Involved in sequence-specific DNA binding transcription factor activity
Specific function:
Nuclear hormone receptor. Involved in the retinoic acid response pathway. Binds 9-cis retinoic acid (9C-RA)
Gene Name:
RXRG
Uniprot ID:
P48443
Molecular weight:
50870.7
General function:
Involved in sequence-specific DNA binding transcription factor activity
Specific function:
Nuclear hormone receptor. Involved in the retinoic acid response pathway. Binds 9-cis retinoic acid (9C-RA). ARF6 acts as a key regulator of the tissue-specific adipocyte P2 (aP2) enhancer
Gene Name:
RXRA
Uniprot ID:
P19793
Molecular weight:
50810.8