Structure of PDB 4gk4 Chain A Binding Site BS01

Receptor Information
>4gk4 Chain A (length=275) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VHEFAKELDATNISIDKVVGAGEFGEVCSGRLKLPSKKEISVAIKTLKVG
YTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLD
SFLRKHDAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNL
VCKVSDFGLSRVLKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYG
ERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKF
EQIVSILDKLIRNPGSLKIITNLLL
Ligand information
Ligand IDL90
InChIInChI=1S/C20H21N7O2/c1-4-5-8-26-14(15-11(2)6-7-13-12(15)9-21-24-13)10-27-16-17(22-19(26)27)25(3)20(29)23-18(16)28/h6-7,9-10H,4-5,8H2,1-3H3,(H,21,24)(H,23,28,29)
InChIKeyDQROUBDXZUEWBE-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CCCCn1c(cn2c1nc3c2C(=O)NC(=O)N3C)c4c(ccc5c4cn[nH]5)C
CACTVS 3.370CCCCn1c(cn2c1nc3N(C)C(=O)NC(=O)c23)c4c(C)ccc5[nH]ncc45
ACDLabs 12.01O=C5c1c(nc4n1cc(c2c(ccc3c2cnn3)C)n4CCCC)N(C(=O)N5)C
FormulaC20 H21 N7 O2
Name8-butyl-1-methyl-7-(5-methyl-1H-indazol-4-yl)-1H-imidazo[2,1-f]purine-2,4(3H,8H)-dione
ChEMBLCHEMBL3774978
DrugBank
ZINCZINC000095921223
PDB chain4gk4 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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PDB4gk4 Optimization of Inhibitors of the Tyrosine Kinase EphB4. 2. Cellular Potency Improvement and Binding Mode Validation by X-ray Crystallography.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		A651 K653 E670 M674 I697 T699 Y701 M702 L753 S763 D764
Binding residue
(residue number reindexed from 1)		A43 K45 E62 M66 I89 T91 Y93 M94 L145 S155 D156
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.85,IC50=14nM
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:4gk4, PDBe:4gk4, PDBj:4gk4
PDBsum4gk4
PubMed23253074
UniProtP29320|EPHA3_HUMAN Ephrin type-A receptor 3 (Gene Name=EPHA3)

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