Structure of PDB 3u6j Chain A Binding Site BS01

Receptor Information
>3u6j Chain A (length=308) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EHCERLPYDASKWEFPRDRLKLGKPLGRGAFGQVIEADAFGIDATCRTVA
VKMLKEGATHSEHRALMSELKILIHIGHHLNVVNLLGACTKPGGPLMVIT
EFCKFGNLSTYLRSKRNEFVPYKVAPEDLYKDFLTLEHLICYSFQVAKGM
EFLASRKCIHRDLAARNILLSEKNVVKICDFGLARDIYKDPDYVRKGDAR
LPLKWMAPETIFDRVYTIQSDVWSFGVLLWEIFSLGASPYPGVKIDEEFC
RRLKEGTRMRAPDYTTPEMYQTMLDCWHGEPSQRPTFSELVEHLGNLLQA
NAQQDRHH
Ligand information
Ligand ID03X
InChIInChI=1S/C29H25FN4O5/c1-17-27(29(36)34(33(17)2)19-8-6-5-7-9-19)28(35)32-18-10-11-24(21(30)14-18)39-23-12-13-31-22-16-26(38-4)25(37-3)15-20(22)23/h5-16H,1-4H3,(H,32,35)
InChIKeySBLMCLDRWJNEJK-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.370COc1cc2nccc(Oc3ccc(NC(=O)C4=C(C)N(C)N(C4=O)c5ccccc5)cc3F)c2cc1OC
OpenEye OEToolkits 1.7.2CC1=C(C(=O)N(N1C)c2ccccc2)C(=O)Nc3ccc(c(c3)F)Oc4ccnc5c4cc(c(c5)OC)OC
ACDLabs 12.01Fc3c(Oc1c2cc(OC)c(OC)cc2ncc1)ccc(c3)NC(=O)C=5C(=O)N(c4ccccc4)N(C=5C)C
FormulaC29 H25 F N4 O5
NameN-{4-[(6,7-dimethoxyquinolin-4-yl)oxy]-3-fluorophenyl}-1,5-dimethyl-3-oxo-2-phenyl-2,3-dihydro-1H-pyrazole-4-carboxamide
ChEMBLCHEMBL2031893
DrugBank
ZINCZINC000071996259
PDB chain3u6j Chain A Residue 1 [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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PDB3u6j Structure-based design of novel class II c-Met inhibitors: 1. Identification of pyrazolone-based derivatives.
Resolution2.15 Å
Binding residue
(original residue number in PDB)		L840 V848 A866 K868 E885 L889 C919 L1019 H1026 L1035 C1045 D1046 F1047
Binding residue
(residue number reindexed from 1)		L26 V34 A50 K52 E69 L73 C103 L153 H160 L169 C179 D180 F181
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.21,IC50=6.2nM
BindingDB: IC50=10nM
Enzymatic activity
Catalytic site (original residue number in PDB) D1028 A1030 R1032 N1033 D1046 K1055 D1064
Catalytic site (residue number reindexed from 1) D162 A164 R166 N167 D180 K189 D198
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:3u6j, PDBe:3u6j, PDBj:3u6j
PDBsum3u6j
PubMed22320343
UniProtP35968|VGFR2_HUMAN Vascular endothelial growth factor receptor 2 (Gene Name=KDR)

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