ChemFOnt: Showing chemical card for 9-cis-Retinoic acid (CFc000001598)

Record Information

Version

1.0

Creation Date

2022-08-28 10:25:12 UTC

Update Date

2022-09-13 18:46:16 UTC

Chemfont ID

CFc000001598

Molecule Identification

Common Name

9-cis-Retinoic acid

Definition

9-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

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
(all-e)-3,7-Dimethyl-9-(2,6,6-trimethyl-1-cyclohexen-1-yl)-2,4,6,8-nonatetraenoate	HMDB
(all-e)-3,7-Dimethyl-9-(2,6,6-trimethyl-1-cyclohexen-1-yl)-2,4,6,8-nonatetraenoic acid	HMDB
3,7-Dimethyl-9-(2,6,6-trimethyl-1-cyclohexen-1-yl)-2,4,6,8-nonatetraenoate	HMDB
3,7-Dimethyl-9-(2,6,6-trimethyl-1-cyclohexen-1-yl)-2,4,6,8-nonatetraenoic acid	HMDB
all-(e)-Retinoate	HMDB
all-(e)-Retinoic acid	HMDB
all-trans-Retinoate	HMDB
all-trans-Tretinoin	HMDB
all-trans-Vitamin a acid	HMDB
all-trans-Vitamin a1 acid	HMDB
beta-Retinoate	HMDB
beta-Retinoic acid	HMDB
Retinoate	HMDB, Generator
Retinoic acid	HMDB
trans-Retinoate	HMDB
trans-Retinoic acid	HMDB
Tretin m	HMDB
Vitamin a acid	HMDB

Chemical Formula

C₂₀H₂₈O₂

Average Molecular Weight

300.4351

Monoisotopic Molecular Weight

300.20893014

IUPAC Name

3,7-dimethyl-9-(2,6,6-trimethylcyclohex-1-en-1-yl)nona-2,4,6,8-tetraenoic acid

Traditional Name

isotretinoin

CAS Registry Number

5300-03-8

SMILES

CC(C=CC1=C(C)CCCC1(C)C)=CC=CC(C)=CC(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)

InChI Key

SHGAZHPCJJPHSC-UHFFFAOYSA-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

retinoid (CHEBI:26536 )
alpha,beta-unsaturated monocarboxylic acid (CHEBI:26536 )

Functional Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 8699330)

Cellular substructure

Extracellular (HMDB: HMDB0002369)
Membrane (HMDB: HMDB0002369)

Source

Exogenous

Exogenous (HMDB: HMDB0002369)

Endogenous

Endogenous (HMDB: HMDB0002369)

Process

Naturally occurring process

Biological process

Biochemical pathway

Metabolic pathway

Retinol Metabolism (HMDB: HMDB0002369)

Disease pathway

Vitamin A Deficiency (PathBank: SMP0120500)

Role

Physical Properties

Predicted 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	36.93 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