Structure of PDB 3efw Chain A Binding Site BS01

Receptor Information
>3efw Chain A (length=240) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RQWALEDFEIGRPLGKGKFGNVYLAREKQSKFILALKVLFKAQLEKAGVE
HQLRREVEIQSHLRHPNILRLYGYFHDATRVYLILEYAPLGTVYRELQKL
SKFDEQRTATYITELANALSYCHSKRVIHRDIKPENLLLGSAGELKIADF
LDYLPPEMIEKVDLWSLGVLCYEFLVGKPPFEANTYQETYKRISRVEFTF
PDFVTEGARDLISRLLKHNPSQRPMLREVLEHPWITANSS
Ligand information
Ligand IDAK8
InChIInChI=1S/C25H21F3N6O2/c1-15-13-18(33-24(35)32-17-6-3-5-16(14-17)25(26,27)28)8-9-21(15)36-22-19(7-4-11-30-22)20-10-12-31-23(29-2)34-20/h3-14H,1-2H3,(H,29,31,34)(H2,32,33,35)
InChIKeyINFGJUQNPPGDNS-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04FC(F)(F)c1cc(ccc1)NC(=O)Nc4ccc(Oc3ncccc3c2nc(ncc2)NC)c(c4)C
OpenEye OEToolkits 1.5.0Cc1cc(ccc1Oc2c(cccn2)c3ccnc(n3)NC)NC(=O)Nc4cccc(c4)C(F)(F)F
CACTVS 3.341CNc1nccc(n1)c2cccnc2Oc3ccc(NC(=O)Nc4cccc(c4)C(F)(F)F)cc3C
FormulaC25 H21 F3 N6 O2
Name1-[3-methyl-4-({3-[2-(methylamino)pyrimidin-4-yl]pyridin-2-yl}oxy)phenyl]-3-[3-(trifluoromethyl)phenyl]urea
ChEMBLCHEMBL468612
DrugBank
ZINCZINC000039187994
PDB chain3efw Chain A Residue 404 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB3efw Pyridyl-pyrimidine benzimidazole derivatives as potent, selective, and orally bioavailable inhibitors of Tie-2 kinase.
Resolution2.29 Å
Binding residue
(original residue number in PDB)		F144 V147 K162 V174 L178 Y212 A213 L263 A273 F275
Binding residue
(residue number reindexed from 1)		F19 V22 K37 V49 L53 Y87 A88 L138 A148 F150
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.40,IC50=4nM
Enzymatic activity
Catalytic site (original residue number in PDB) D256 K258 E260 N261 D274
Catalytic site (residue number reindexed from 1) D131 K133 E135 N136 D149
Enzyme Commision number 2.7.11.1: non-specific serine/threonine protein kinase.
Gene Ontology
Molecular Function
GO:0004672 protein kinase activity
GO:0005524 ATP binding
Biological Process
GO:0000212 meiotic spindle organization
GO:0000226 microtubule cytoskeleton organization
GO:0000278 mitotic cell cycle
GO:0006468 protein phosphorylation
GO:0007052 mitotic spindle organization
GO:0007098 centrosome cycle
GO:0007100 mitotic centrosome separation
GO:0051321 meiotic cell cycle

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3efw, PDBe:3efw, PDBj:3efw
PDBsum3efw
PubMed19062275
UniProtO14965|AURKA_HUMAN Aurora kinase A (Gene Name=AURKA)

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