Structure of PDB 3dtw Chain A Binding Site BS01

Receptor Information
>3dtw Chain A (length=288) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ERLPYDASKWEFPRDRLKLGKPLGRGGQVIEADAFGIDKTCRTVAVKMLK
EGATHSEHRALMSELKILIHIGHHLNVVNLLGACTKPGGPLMVITEFCKF
GNLSTYLRSKRNEFVPYKVAPEDLYKDFLTLEHLICYSFQVAKGMEFLAS
RKCIHRDLAARNILLSEKNVVKICDFLPLKWMAPETIFDRVYTIQSDVWS
FGVLLWEIFSLGASPYPGVKIDEEFCRRLKEGTRMRAPDYTTPEMYQTML
DCWHGEPSQRPTFSELVEHLGNLLQANAQQDRHHHHHH
Ligand information
Ligand IDA96
InChIInChI=1S/C19H11ClF3N5O2/c20-14-5-4-13-16(15(14)18(29)27-12-7-24-9-25-8-12)30-28-17(13)26-11-3-1-2-10(6-11)19(21,22)23/h1-9H,(H,26,28)(H,27,29)
InChIKeyFEGRQUWSKADGSP-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1cc(cc(c1)Nc2c3ccc(c(c3on2)C(=O)Nc4cncnc4)Cl)C(F)(F)F
ACDLabs 10.04FC(F)(F)c1cc(ccc1)Nc3noc2c(c(Cl)ccc23)C(=O)Nc4cncnc4
CACTVS 3.341FC(F)(F)c1cccc(Nc2noc3c2ccc(Cl)c3C(=O)Nc4cncnc4)c1
FormulaC19 H11 Cl F3 N5 O2
Name6-chloro-N-pyrimidin-5-yl-3-{[3-(trifluoromethyl)phenyl]amino}-1,2-benzisoxazole-7-carboxamide
ChEMBLCHEMBL491429
DrugBankDB07326
ZINCZINC000020149010
PDB chain3dtw Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3dtw Discovery of amido-benzisoxazoles as potent c-Kit inhibitors.
Resolution2.9 Å
Binding residue
(original residue number in PDB)		A866 K868 E885 L889 T916 C919 L1035 C1045 D1046
Binding residue
(residue number reindexed from 1)		A45 K47 E64 L68 T95 C98 L164 C174 D175
Annotation score1
Binding affinityBindingDB: IC50=353nM
Enzymatic activity
Catalytic site (original residue number in PDB) D1028 A1030 R1032 N1033 D1046
Catalytic site (residue number reindexed from 1) D157 A159 R161 N162 D175
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:0004714 transmembrane receptor protein tyrosine kinase activity
GO:0005524 ATP binding
Biological Process
GO:0006468 protein phosphorylation
GO:0007169 cell surface receptor protein tyrosine kinase signaling pathway

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3dtw, PDBe:3dtw, PDBj:3dtw
PDBsum3dtw
PubMed18723346
UniProtP35968|VGFR2_HUMAN Vascular endothelial growth factor receptor 2 (Gene Name=KDR)

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