Structure of PDB 2x9f Chain A Binding Site BS01

Receptor Information
>2x9f 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]
KEIDVSYVKIEEVIGAGEFGEVCRGRLKAPGKKESCVAIKTLYTERQRRE
FLSEASIMGQFEHPNIIRLEGVVTNSMPVMILTEFMENGALDSFLRLNDG
QFTVIQLVGMLRGIASGMRYLAEMSYVHRDLAARNILVNSNLVCKVSDFG
LSRFLGGKIPIRWTAPEAIAFRKFTSASDAWSYGIVMWEVMSFGERPYWD
MSNQDVINAIEQDYRLPPPPDCPTSLHQLMLDCWQKDRNARPRFPQVVSA
LDKMIRNPASLKIVA
Ligand information
Ligand IDX9F
InChIInChI=1S/C18H16N6O2S/c1-27(25,26)13-5-2-4-12(10-13)21-18-19-9-8-17(23-18)22-15-6-3-7-16-14(15)11-20-24-16/h2-11H,1H3,(H,20,24)(H2,19,21,22,23)
InChIKeyFIWCLCRWDUELGO-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.352C[S](=O)(=O)c1cccc(Nc2nccc(Nc3cccc4[nH]ncc34)n2)c1
ACDLabs 10.04O=S(=O)(c1cccc(c1)Nc2nccc(n2)Nc3cccc4c3cnn4)C
OpenEye OEToolkits 1.6.1CS(=O)(=O)c1cccc(c1)Nc2nccc(n2)Nc3cccc4c3cn[nH]4
FormulaC18 H16 N6 O2 S
NameN^4^-1H-INDAZOL-4-YL-N^2^-[3-(METHYLSULFONYL)PHENYL]PYRIMIDINE-2,4-DIAMINE
ChEMBLCHEMBL1236772
DrugBank
ZINCZINC000034840816
PDB chain2x9f 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]
PDB2x9f Inhibitors of the Tyrosine Kinase Ephb4. Part 3: Identification of Non-Benzodioxole-Based Kinase Inhibitors.
Resolution1.75 Å
Binding residue
(original residue number in PDB)		I621 A645 K647 E664 T693 F695 M696 E697 G699 L747 S757 D758
Binding residue
(residue number reindexed from 1)		I14 A38 K40 E54 T83 F85 M86 E87 G89 L137 S147 D148
Annotation score1
Binding affinityMOAD: ic50=0.061uM
PDBbind-CN: -logKd/Ki=7.21,IC50=61nM
BindingDB: IC50=61nM
Enzymatic activity
Catalytic site (original residue number in PDB) D740 A742 R744 N745 D758 K781 P783
Catalytic site (residue number reindexed from 1) D130 A132 R134 N135 D148 K158 P160
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:2x9f, PDBe:2x9f, PDBj:2x9f
PDBsum2x9f
PubMed20850301
UniProtP54760|EPHB4_HUMAN Ephrin type-B receptor 4 (Gene Name=EPHB4)

[Back to BioLiP]