Structure of PDB 4gk2 Chain A Binding Site BS01

Receptor Information
>4gk2 Chain A (length=265) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VHEFAKELDATNISIDKVVGAGEFGEVCSGRLKLPSKKEISVAIKTLKVG
YTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLD
SFLRKHDAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNL
VCKVSDFGLPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWE
MSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSI
LDKLIRLKIITNLLL
Ligand information
Ligand IDL66
InChIInChI=1S/C22H19N5O4/c1-12-8-9-13(28)10-14(12)16-11-26-18-19(25(2)22(30)24-20(18)29)23-21(26)27(16)15-6-4-5-7-17(15)31-3/h4-11,28H,1-3H3,(H,24,29,30)
InChIKeyJTWMOWRMSZZHDR-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6Cc1ccc(cc1c2cn3c4c(nc3n2c5ccccc5OC)N(C(=O)NC4=O)C)O
CACTVS 3.370COc1ccccc1n2c(cn3c2nc4N(C)C(=O)NC(=O)c34)c5cc(O)ccc5C
ACDLabs 12.01O=C2c1n4c(nc1N(C(=O)N2)C)n(c(c3cc(O)ccc3C)c4)c5ccccc5OC
FormulaC22 H19 N5 O4
Name7-(5-hydroxy-2-methylphenyl)-8-(2-methoxyphenyl)-1-methyl-1H-imidazo[2,1-f]purine-2,4(3H,8H)-dione
ChEMBLCHEMBL566515
DrugBank
ZINCZINC000045245466
PDB chain4gk2 Chain A Residue 1001 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4gk2 Optimization of Inhibitors of the Tyrosine Kinase EphB4. 2. Cellular Potency Improvement and Binding Mode Validation by X-ray Crystallography.
Resolution2.195 Å
Binding residue
(original residue number in PDB)		V635 A651 K653 E670 T699 Y701 M702 G705 L753 D764
Binding residue
(residue number reindexed from 1)		V27 A43 K45 E62 T91 Y93 M94 G97 L145 D156
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.80,IC50=1.6nM
BindingDB: IC50=40nM
Enzymatic activity
Catalytic site (original residue number in PDB) D746 A748 R750 N751 D764
Catalytic site (residue number reindexed from 1) D138 A140 R142 N143 D156
Enzyme Commision number 2.7.10.1: receptor protein-tyrosine kinase.
Gene Ontology
Molecular Function
GO:0004672 protein kinase activity
GO:0004713 protein tyrosine kinase activity
GO:0005524 ATP binding
Biological Process
GO:0006468 protein phosphorylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4gk2, PDBe:4gk2, PDBj:4gk2
PDBsum4gk2
PubMed23253074
UniProtP29320|EPHA3_HUMAN Ephrin type-A receptor 3 (Gene Name=EPHA3)

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