Structure of PDB 2vx1 Chain A Binding Site BS01

Receptor Information
>2vx1 Chain A (length=274) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KEIDVSYVKIEEVIGAGEFGEVCRGRLKAPGKKESCVAIKTLKGGYTERQ
RREFLSEASIMGQFEHPNIIRLEGVVTNSMPVMILTEFMENGALDSFLRL
NDGQFTVIQLVGMLRGIASGMRYLAEMSYVHRDLAARNILVNSNLVCKVS
DFGLSRFLEENSSDGGKIPIRWTAPEAIAFRKFTSASDAWSYGIVMWEVM
SFGERPYWDMSNQDVINAIEQDYRLPPPPDCPTSLHQLMLDCWQKDRNAR
PRFPQVVSALDKMIRNPASLKIVA
Ligand information
Ligand ID7X8
InChIInChI=1S/C18H14ClN5O3/c19-12-4-5-13-16(27-9-26-13)15(12)23-14-6-7-21-18(24-14)22-11-3-1-2-10(8-11)17(20)25/h1-8H,9H2,(H2,20,25)(H2,21,22,23,24)
InChIKeyZVQZIVCQLFGXFZ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1cc(cc(c1)Nc2nccc(n2)Nc3c(ccc4c3OCO4)Cl)C(=O)N
ACDLabs 10.04O=C(N)c1cc(ccc1)Nc2nccc(n2)Nc3c(Cl)ccc4OCOc34
CACTVS 3.341NC(=O)c1cccc(Nc2nccc(Nc3c(Cl)ccc4OCOc34)n2)c1
FormulaC18 H14 Cl N5 O3
Name3-({4-[(5-CHLORO-1,3-BENZODIOXOL-4-YL)AMINO]PYRIMIDIN-2-YL}AMINO)BENZAMIDE
ChEMBLCHEMBL500724
DrugBankDB07256
ZINCZINC000034285196
PDB chain2vx1 Chain A Residue 1889 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB2vx1 Inhibitors of the Tyrosine Kinase Ephb4. Part 2: Structure-Based Discovery and Optimisation of 3,5-Bis Substituted Anilinopyrimidines.
Resolution1.65 Å
Binding residue
(original residue number in PDB)		I621 A645 K647 E664 I691 T693 M696 G699 L747 S757
Binding residue
(residue number reindexed from 1)		I14 A38 K40 E57 I84 T86 M89 G92 L140 S150
Annotation score1
Binding affinityMOAD: ic50=0.22uM
PDBbind-CN: -logKd/Ki=6.66,IC50=0.220uM
BindingDB: IC50=900nM
Enzymatic activity
Catalytic site (original residue number in PDB) D740 A742 R744 N745 D758 K781 P783
Catalytic site (residue number reindexed from 1) D133 A135 R137 N138 D151 K167 P169
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:2vx1, PDBe:2vx1, PDBj:2vx1
PDBsum2vx1
PubMed18851911
UniProtP54760|EPHB4_HUMAN Ephrin type-B receptor 4 (Gene Name=EPHB4)

[Back to BioLiP]