Structure of PDB 3cbs Chain A Binding Site BS01

Receptor Information
>3cbs Chain A (length=137) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PNFSGNWKIIRSENFEELLKVLGVNVMLRKIAVAAASKPAVEIKQEGDTF
YIKTSTTVRTTEINFKVGEEFEEQTVDGRPCKSLVKWESENKMVCEQKLL
KGEGPKTSWTRELTNDGELILTMTADDVVCTRVYVRE
Ligand information
Ligand IDR12
InChIInChI=1S/C20H24O3/c1-13(7-6-8-14(2)11-20(22)23)9-10-18-15(3)12-19(21)17(5)16(18)4/h6-12,21H,1-5H3,(H,22,23)/b8-6+,10-9+,13-7+,14-11+
InChIKeyCAAFTBWHFUPDGX-OFCLTBKTSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.2Cc1cc(c(c(c1/C=C/C(=C/C=C/C(=C/C(=O)O)/C)/C)C)C)O
CACTVS 3.370CC(=C/C=C/C(C)=C/C(O)=O)\C=C\c1c(C)cc(O)c(C)c1C
ACDLabs 12.01O=C(O)\C=C(\C=C\C=C(\C=C\c1c(cc(O)c(c1C)C)C)C)C
OpenEye OEToolkits 1.7.2Cc1cc(c(c(c1C=CC(=CC=CC(=CC(=O)O)C)C)C)C)O
CACTVS 3.370CC(=CC=CC(C)=CC(O)=O)C=Cc1c(C)cc(O)c(C)c1C
FormulaC20 H24 O3
Name(2E,4E,6E,8E)-9-(4-hydroxy-2,3,6-trimethylphenyl)-3,7-dimethylnona-2,4,6,8-tetraenoic acid
ChEMBL
DrugBankDB08455
ZINC
PDB chain3cbs Chain A Residue 200 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3cbs Structures of cellular retinoic acid binding proteins I and II in complex with synthetic retinoids.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		L28 A36 T54 V58 L121 R132 Y134
Binding residue
(residue number reindexed from 1)		L28 A36 T54 V58 L121 R132 Y134
Annotation score1
Binding affinityMOAD: ic50=58nM
PDBbind-CN: -logKd/Ki=7.24,IC50=58nM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0001972 retinoic acid binding
GO:0005501 retinoid binding
GO:0005504 fatty acid binding
GO:0005515 protein binding
GO:0008289 lipid binding
GO:0016918 retinal binding
GO:0019841 retinol binding
GO:0030332 cyclin binding
Biological Process
GO:0006355 regulation of DNA-templated transcription
GO:0007165 signal transduction
GO:0008544 epidermis development
GO:0015908 fatty acid transport
GO:0035115 embryonic forelimb morphogenesis
GO:0042573 retinoic acid metabolic process
GO:0048672 positive regulation of collateral sprouting
Cellular Component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005783 endoplasmic reticulum
GO:0005829 cytosol
GO:0070062 extracellular exosome

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3cbs, PDBe:3cbs, PDBj:3cbs
PDBsum3cbs
PubMed10531482
UniProtP29373|RABP2_HUMAN Cellular retinoic acid-binding protein 2 (Gene Name=CRABP2)

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