Showing metabocard for 13-cis-Retinoic acid (BMDB0006219)

IdentificationTaxonomyPhysical propertiesPathwaysSpectraConcentrationsLinksReferencesenzymes (14) Show 14 proteinsXML
Record Information
Version1.0
Creation Date2016-09-30 23:20:29 UTC
Update Date2020-04-22 15:16:57 UTC
BMDB IDBMDB0006219
Secondary Accession Numbers
  • BMDB06219
Metabolite Identification
Common Name13-cis-Retinoic acid
Description13-cis-Retinoic acid, also known as isotretinoina or accutane, 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. 13-cis-Retinoic acid is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral.
Structure
Thumb
MOLSDFPDBSMILESInChI
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
StatusExpected but not Quantified
Origin
  • Endogenous
  • Exogenous
BiofunctionNot Available
ApplicationNot Available
Cellular locations
  • Cell membrane
  • Cytoplasm
  • Endoplasmic reticulum
  • Membrane
  • Nucleus
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
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 FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-052r-2090000000-42b8aa0666b5a088671bView in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positivesplash10-0a4i-5139000000-29caedb85908ca2b99f4View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableView in JSpectraViewer
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
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0uei-0494000000-28e6366fdd47e8ba2117View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-052r-2980000000-3e7fc78de83c23830416View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-052r-5900000000-ef4d86f8bcf86959f794View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-052b-0090000000-e07ffb4c1e5c63ab1b59View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-052b-0090000000-a0a8411213bbd2543243View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-000i-3690000000-97e6a74798dd69c30ad1View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0zir-0973000000-3040e9e4a1a5448efbcbView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-060c-1950000000-f3b9c9b378f60b8c49a9View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0ar3-5910000000-de22eb65f274483f3f98View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-052b-0090000000-5f942e3b870e7bd0121bView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0a4i-0190000000-22b445382d3977280045View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-016r-4900000000-0005b37f6d54a42a84f6View in MoNA
1D NMR1H NMR Spectrum (1D, 600 MHz, CDCl3, experimental)Not AvailableView in JSpectraViewer
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, CDCl3, experimental)Not AvailableView in JSpectraViewer
Biological Properties
Cellular Locations
  • Cell membrane
  • Cytoplasm
  • Endoplasmic reticulum
  • Membrane
  • Nucleus
Biospecimen LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
HMDB IDHMDB0006219
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
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available

Enzymes

Enzyme Details
1. Prostaglandin-H2 D-isomerase
General function:
Involved in prostaglandin-D synthase activity
Specific function:
Catalyzes the conversion of PGH2 to PGD2, a prostaglandin involved in smooth muscle contraction/relaxation and a potent inhibitor of platelet aggregation. Involved in a variety of CNS functions, such as sedation, NREM sleep and PGE2-induced allodynia, and may have an anti-apoptotic role in oligodendrocytes. Binds small non-substrate lipophilic molecules, including biliverdin, bilirubin, retinal, retinoic acid and thyroid hormone, and may act as a scavenger for harmful hydrophobic molecules and as a secretory retinoid and thyroid hormone transporter. Possibly involved in development and maintenance of the blood-brain, blood-retina, blood-aqueous humor and blood-testis barrier. It is likely to play important roles in both maturation and maintenance of the central nervous system and male reproductive system (By similarity).
Gene Name:
PTGDS
Uniprot ID:
O02853
Molecular weight:
21229.0
Enzyme Details
2. Retinal dehydrogenase 1
General function:
Energy production and conversion
Specific function:
Can convert/oxidize retinaldehyde to retinoic acid. Binds free retinal and cellular retinol-binding protein-bound retinal. May have a broader specificity and oxidize other aldehydes in vivo.
Gene Name:
ALDH1A1
Uniprot ID:
P48644
Molecular weight:
54806.0
Enzyme Details
3. Polycomb group RING finger protein 1
General function:
Transcription
Specific function:
Component of the Polycomb group (PcG) multiprotein BCOR complex, a complex required to maintain the transcriptionally repressive state of some genes, such as BCL6 and the cyclin-dependent kinase inhibitor, CDKN1A. Transcriptional repressor that may be targeted to the DNA by BCL6; this transcription repressor activity may be related to PKC signaling pathway. Represses CDKN1A expression by binding to its promoter, and this repression is dependent on the retinoic acid response element (RARE element). Promotes cell cycle progression and enhances cell proliferation as well. May have a positive role in tumor cell growth by down-regulating CDKN1A. Component of a Polycomb group (PcG) multiprotein PRC1-like complex, a complex class required to maintain the transcriptionally repressive state of many genes, including Hox genes, throughout development. PcG PRC1 complex acts via chromatin remodeling and modification of histones; it mediates monoubiquitination of histone H2A 'Lys-119', rendering chromatin heritably changed in its expressibility. Within the PRC1-like complex, regulates RNF2 ubiquitin ligase activity. Regulates the expression of DPPA4 and NANOG in the NT2 embryonic carcinoma cells.
Gene Name:
PCGF1
Uniprot ID:
Q2YDF9
Molecular weight:
30324.0
Enzyme Details
4. Retinoic acid receptor responder (Tazarotene induced) 1
General function:
Involved in receptor activity
Specific function:
Not Available
Gene Name:
RARRES1
Uniprot ID:
Q0P5D6
Molecular weight:
32771.0
Enzyme Details
5. Retinoic acid receptor beta
General function:
Involved in retinoic acid receptor activity
Specific function:
Not Available
Gene Name:
Not Available
Uniprot ID:
Q45UD6
Molecular weight:
10459.0
Enzyme Details
6. Retinoic acid receptor responder protein 2
General function:
Not Available
Specific function:
Adipocyte-secreted protein (adipokine) that regulates adipogenesis, metabolism and inflammation through activation of the chemokine-like receptor 1 (CMKLR1). Its other ligands include G protein-coupled receptor 1 (GPR1) and chemokine receptor-like 2 (CCRL2). Positively regulates adipocyte differentiation, modulates the expression of adipocyte genes involved in lipid and glucose metabolism and might play a role in angiogenesis, a process essential for the expansion of white adipose tissue. Also acts as a proinflammatory adipokine, causing an increase in secretion of proinflammatory and prodiabetic adipokines, which further impair adipose tissue metabolic function and have negative systemic effects including impaired insulin sensitivity, altered glucose and lipid metabolism, and a decrease in vascular function in other tissues. Can have both pro- and anti-inflammatory properties depending on the modality of enzymatic cleavage by different classes of proteases. Acts as a chemotactic factor for leukocyte populations expressing CMKLR1, particularly immature plasmacytoid dendritic cells, but also immature myeloid DCs, macrophages and natural killer cells. Exerts an anti-inflammatory role by preventing TNF/TNFA-induced VCAM1 expression and monocytes adhesion in vascular endothelial cells. The effect is mediated via inhibiting activation of NF-kappa-B and CRK/p38 through stimulation of AKT1/NOS3 signaling and nitric oxide production. Exhibits an antimicrobial function in the skin (By similarity).
Gene Name:
RARRES2
Uniprot ID:
Q29RS5
Molecular weight:
18357.0
Enzyme Details
7. Retinoic acid receptor, alpha
General function:
Involved in retinoic acid receptor activity
Specific function:
Not Available
Gene Name:
RARA
Uniprot ID:
Q58DG3
Molecular weight:
30654.0
Enzyme Details
8. RARG protein
General function:
Involved in retinoic acid receptor activity
Specific function:
Not Available
Gene Name:
RARG
Uniprot ID:
Q08DD4
Molecular weight:
50946.0
Enzyme Details
9. Peroxisome proliferator-activated receptor gamma
General function:
Involved in protein binding
Specific function:
Nuclear receptor that binds peroxisome proliferators such as hypolipidemic drugs and fatty acids. Once activated by a ligand, the nuclear receptor binds to DNA specific PPAR response elements (PPRE) and modulates the transcription of its target genes, such as acyl-CoA oxidase. It therefore controls the peroxisomal beta-oxidation pathway of fatty acids. Key regulator of adipocyte differentiation and glucose homeostasis. ARF6 acts as a key regulator of the tissue-specific adipocyte P2 (aP2) enhancer. Acts as a critical regulator of gut homeostasis by suppressing NF-kappa-B-mediated proinflammatory responses. Plays a role in the regulation of cardiovascular circadian rhythms by regulating the transcription of ARNTL/BMAL1 in the blood vessels.
Gene Name:
PPARG
Uniprot ID:
O18971
Molecular weight:
57579.0
Enzyme Details
10. Fatty acid-binding protein, adipocyte
General function:
Involved in lipid binding
Specific function:
Lipid transport protein in adipocytes. Binds both long chain fatty acids and retinoic acid. Delivers long-chain fatty acids and retinoic acid to their cognate receptors in the nucleus.
Gene Name:
FABP4
Uniprot ID:
P48035
Molecular weight:
14678.0
Enzyme Details
11. Cellular retinoic acid-binding protein 1
General function:
Involved in retinal binding
Specific function:
Cytosolic CRABPs may regulate the access of retinoic acid to the nuclear retinoic acid receptors.
Gene Name:
CRABP1
Uniprot ID:
P62964
Molecular weight:
15592.0
Enzyme Details
12. LOC100138545 protein
General function:
Involved in SMAD binding
Specific function:
Not Available
Gene Name:
LOC100138545
Uniprot ID:
A6QQE3
Molecular weight:
91118.0
Enzyme Details
13. Retinoic acid receptor RXR-gamma
General function:
Involved in steroid binding
Specific function:
Receptor for retinoic acid. Retinoic acid receptors bind as heterodimers to their target response elements in response to their ligands, all-trans or 9-cis retinoic acid, and regulate gene expression in various biological processes. The RAR/RXR heterodimers bind to the retinoic acid response elements (RARE) composed of tandem 5'-AGGTCA-3' sites known as DR1-DR5. The high affinity ligand for RXRs is 9-cis retinoic acid (By similarity).
Gene Name:
RXRG
Uniprot ID:
Q0VC20
Molecular weight:
50882.0
Enzyme Details
14. Cellular retinoic acid-binding protein 2
General function:
Involved in retinal binding
Specific function:
Transports retinoic acid to the nucleus. Regulates the access of retinoic acid to the nuclear retinoic acid receptors (By similarity).
Gene Name:
CRABP2
Uniprot ID:
Q5PXY7
Molecular weight:
15735.0