Structure of PDB 2vww Chain A Binding Site BS01

Receptor Information
>2vww Chain A (length=253) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EIDVSYVKIEEVIGAGEFGEVCRGRLKAPGKKESCVAIKTLTERQRREFL
SEASIMGQFEHPNIIRLEGVVTNSMPVMILTEFMENGALDSFLRLNDGQF
TVIQLVGMLRGIASGMRYLAEMSYVHRDLAARNILVNSNLVCKVSDFIPI
RWTAPEAIAFRKFTSASDAWSYGIVMWEVMSFGERPYWDMSNQDVINAIE
QDYRLPPPPDCPTSLHQLMLDCWQKDRNARPRFPQVVSALDKMIRNPASL
KIV
Ligand information
Ligand ID7X2
InChIInChI=1S/C20H19ClN4O5/c1-26-14-8-11(9-15(27-2)18(14)28-3)23-20-22-7-6-16(25-20)24-17-12(21)4-5-13-19(17)30-10-29-13/h4-9H,10H2,1-3H3,(H2,22,23,24,25)
InChIKeyHMKLUOPMOJOUDZ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0COc1cc(cc(c1OC)OC)Nc2nccc(n2)Nc3c(ccc4c3OCO4)Cl
ACDLabs 10.04Clc1ccc4OCOc4c1Nc2nc(ncc2)Nc3cc(OC)c(OC)c(OC)c3
CACTVS 3.341COc1cc(Nc2nccc(Nc3c(Cl)ccc4OCOc34)n2)cc(OC)c1OC
FormulaC20 H19 Cl N4 O5
NameN'-(5-CHLORO-1,3-BENZODIOXOL-4-YL)-N-(3,4,5- TRIMETHOXYPHENYL)PYRIMIDINE-2,4-DIAMINE
ChEMBLCHEMBL256725
DrugBankDB07250
ZINCZINC000016052641
PDB chain2vww Chain A Residue 1888 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2vww Inhibitors of the Tyrosine Kinase Ephb4. Part 1: Structure-Based Design and Optimization of a Series of 2,4-Bis-Anilinopyrimidines
Resolution1.9 Å
Binding residue
(original residue number in PDB)		I621 A645 K647 E664 I677 I691 T693 M696 G699 A700 L747 S757
Binding residue
(residue number reindexed from 1)		I13 A37 K39 E52 I65 I79 T81 M84 G87 A88 L135 S145
Annotation score1
Binding affinityMOAD: ic50=0.24uM
PDBbind-CN: -logKd/Ki=6.62,IC50=0.24uM
BindingDB: IC50=240nM
Enzymatic activity
Catalytic site (original residue number in PDB) D740 A742 R744 N745 D758 P783
Catalytic site (residue number reindexed from 1) D128 A130 R132 N133 D146 P149
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:2vww, PDBe:2vww, PDBj:2vww
PDBsum2vww
PubMed18434142
UniProtP54760|EPHB4_HUMAN Ephrin type-B receptor 4 (Gene Name=EPHB4)

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