Structure of PDB 4gk3 Chain A Binding Site BS01

Receptor Information
>4gk3 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
VCKVSDFGLSRVLIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGE
RPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFE
QIVSILDKLIRNPGSLKIITSNLLL
Ligand information
Ligand IDL87
InChIInChI=1S/C19H21N5O2/c1-4-5-10-23-14(13-9-7-6-8-12(13)2)11-24-15-16(20-18(23)24)22(3)19(26)21-17(15)25/h6-9,11H,4-5,10H2,1-3H3,(H,21,25,26)
InChIKeyKCEWOOVCWCPFCY-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.370CCCCn1c(cn2c1nc3N(C)C(=O)NC(=O)c23)c4ccccc4C
OpenEye OEToolkits 1.7.6CCCCn1c(cn2c1nc3c2C(=O)NC(=O)N3C)c4ccccc4C
ACDLabs 12.01O=C2c1n4c(nc1N(C(=O)N2)C)n(c(c3ccccc3C)c4)CCCC
FormulaC19 H21 N5 O2
Name8-butyl-1-methyl-7-(2-methylphenyl)-1H-imidazo[2,1-f]purine-2,4(3H,8H)-dione
ChEMBLCHEMBL2333603
DrugBank
ZINCZINC000095587400
PDB chain4gk3 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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PDB4gk3 Optimization of Inhibitors of the Tyrosine Kinase EphB4. 2. Cellular Potency Improvement and Binding Mode Validation by X-ray Crystallography.
Resolution1.898 Å
Binding residue
(original residue number in PDB)		A651 K653 E670 M674 T699 Y701 M702 G705 L753 S763
Binding residue
(residue number reindexed from 1)		A43 K45 E62 M66 T91 Y93 M94 G97 L145 S155
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.25,IC50=56nM
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

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Molecular Function
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Biological Process
External links
PDB RCSB:4gk3, PDBe:4gk3, PDBj:4gk3
PDBsum4gk3
PubMed23253074
UniProtP29320|EPHA3_HUMAN Ephrin type-A receptor 3 (Gene Name=EPHA3)

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