Structure of PDB 8gd2 Chain B Binding Site BS01

Receptor Information
>8gd2 Chain B (length=139) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PVDFTGYWKMLVNENFEEYLRALDVNVALRKIANLLKPDKEIVQDGDHMI
IRTLSTFRNYIMDFQVGKEFEEDLTGIDDRKCMTTVSWDGDKLQCVQKGE
KEGRGWTQWIEGDELHLEMRVEGVVCKQVFKKVQHHHHH
Ligand information
Ligand IDZ5H
InChIInChI=1S/C21H25N3OS/c1-16-7-9-17(10-8-16)21(11-3-4-12-21)20-22-19(25-23-20)15-24(2)14-18-6-5-13-26-18/h5-10,13H,3-4,11-12,14-15H2,1-2H3
InChIKeyGPXYCFQNEZDPGQ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7Cc1ccc(cc1)C2(CCCC2)c3nc(on3)CN(C)Cc4cccs4
CACTVS 3.385CN(Cc1onc(n1)C2(CCCC2)c3ccc(C)cc3)Cc4sccc4
ACDLabs 12.01CN(Cc1nc(no1)C1(CCCC1)c1ccc(C)cc1)Cc1cccs1
FormulaC21 H25 N3 O S
NameN-methyl-1-{3-[1-(4-methylphenyl)cyclopentyl]-1,2,4-oxadiazol-5-yl}-N-[(thiophen-2-yl)methyl]methanamine
ChEMBL
DrugBank
ZINC
PDB chain8gd2 Chain B Residue 201 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8gd2 Discovery of Nonretinoid Inhibitors of CRBP1: Structural and Dynamic Insights for Ligand-Binding Mechanisms.
Resolution1.13 Å
Binding residue
(original residue number in PDB)		F16 K40 T53 Y60 M62 I77 W106 M119
Binding residue
(residue number reindexed from 1)		F16 K40 T53 Y60 M62 I77 W106 M119
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
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:1904768 all-trans-retinol binding
Biological Process
GO:0002138 retinoic acid biosynthetic process
GO:0006776 vitamin A metabolic process
GO:0015908 fatty acid transport
GO:0055088 lipid homeostasis
Cellular Component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005811 lipid droplet
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8gd2, PDBe:8gd2, PDBj:8gd2
PDBsum8gd2
PubMed37713257
UniProtP09455|RET1_HUMAN Retinol-binding protein 1 (Gene Name=RBP1)

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