Structure of PDB 2xvd Chain A Binding Site BS01

Receptor Information
>2xvd Chain A (length=270) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AKEIDVSYVKIEEVIGAGEFGEVCRGRLKAPGKKESCVAIKTLYTERQRR
EFLSEASIMGQFEHPNIIRLEGVVTNSMPVMILTEFMENGALDSFLRLND
GQFTVIQLVGMLRGIASGMRYLAEMSYVHRDLAARNILVNSNLVCKVSDF
GLSRFLESSLGGKIPIRWTAPEAIAFRKFTSASDAWSYGIVMWEVMSFGE
RPYWDMSNQDVINAIEQDYRLPPPPDCPTSLHQLMLDCWQKDRNARPRFP
QVVSALDKMIRNPASLKIVA
Ligand information
Ligand IDAS6
InChIInChI=1S/C26H33N5O4S/c1-18(2)31(24-13-20(17-32)6-5-19(24)3)25-7-8-27-26(29-25)28-21-14-22(30-9-11-35-12-10-30)16-23(15-21)36(4,33)34/h5-8,13-16,18,32H,9-12,17H2,1-4H3,(H,27,28,29)
InChIKeyAAXNCGQOXAXDOW-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.6.1Cc1ccc(cc1N(c2ccnc(n2)Nc3cc(cc(c3)S(=O)(=O)C)N4CCOCC4)C(C)C)CO
CACTVS 3.352CC(C)N(c1ccnc(Nc2cc(cc(c2)[S](C)(=O)=O)N3CCOCC3)n1)c4cc(CO)ccc4C
ACDLabs 10.04O=S(=O)(c3cc(cc(Nc2nc(N(c1cc(ccc1C)CO)C(C)C)ccn2)c3)N4CCOCC4)C
FormulaC26 H33 N5 O4 S
Name{4-METHYL-3-[(1-METHYLETHYL)(2-{[3-(METHYLSULFONYL)-5-MORPHOLIN-4-YLPHENYL]AMINO}PYRIMIDIN-4-YL)AMINO]PHENYL}METHANOL
ChEMBLCHEMBL1738764
DrugBank
ZINCZINC000066167000
PDB chain2xvd Chain A Residue 1889 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2xvd Inhibitors of the Tyrosine Kinase Ephb4. Part 4: Discovery and Optimization of a Benzylic Alcohol Series.
Resolution1.7 Å
Binding residue
(original residue number in PDB)		I621 V629 A645 K647 E664 T693 M696 E697 G699 L747 S757 D758
Binding residue
(residue number reindexed from 1)		I15 V23 A39 K41 E55 T84 M87 E88 G90 L138 S148 D149
Annotation score1
Binding affinityMOAD: ic50=0.002uM
PDBbind-CN: -logKd/Ki=8.70,IC50=0.002uM
BindingDB: IC50=7nM
Enzymatic activity
Catalytic site (original residue number in PDB) D740 A742 R744 N745 D758 K781 P783
Catalytic site (residue number reindexed from 1) D131 A133 R135 N136 D149 K163 P165
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:2xvd, PDBe:2xvd, PDBj:2xvd
PDBsum2xvd
PubMed21441027
UniProtP54760|EPHB4_HUMAN Ephrin type-B receptor 4 (Gene Name=EPHB4)

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