Structure of PDB 4agc Chain A Binding Site BS01

Receptor Information
>4agc Chain A (length=304) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
YLSIVMDPDELPLPYDASKWEFPRDRLKLGKPLGRGAFGQVIEADAFGID
KTATCRTVAVKMLKEGATHSEHRALMSELKILIHIGHHLNVVNLLGACTK
PGGPLMVIVEFCKFGNLSTYLRSKRNEFVPYYKDFLTLEHLICYSFQVAK
GMEFLASRKCIHRDLAARNILLSEKNVVKICDFGLARDIYKDPDYVRKGD
ARLPLKWMAPETIFDRVYTIQSDVWSFGVLLWEIFSLGASPYPGVKIDEE
FCRRLKEGTRMRAPDYTTPEMYQTMLDCWHGEPSQRPTFSELVEHLGNLL
QANA
Ligand information
Ligand IDAXI
InChIInChI=1S/C22H18N4OS/c1-23-22(27)18-7-2-3-8-21(18)28-16-10-11-17-19(25-26-20(17)14-16)12-9-15-6-4-5-13-24-15/h2-14H,1H3,(H,23,27)(H,25,26)/b12-9+
InChIKeyRITAVMQDGBJQJZ-FMIVXFBMSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CNC(=O)c1ccccc1Sc2ccc3c([nH]nc3C=Cc4ccccn4)c2
CACTVS 3.385CNC(=O)c1ccccc1Sc2ccc3c([nH]nc3\C=C\c4ccccn4)c2
OpenEye OEToolkits 2.0.7CNC(=O)c1ccccc1Sc2ccc3c(c2)[nH]nc3/C=C/c4ccccn4
ACDLabs 12.01O=C(NC)c4ccccc4Sc2ccc3c(\C=C\c1ncccc1)nnc3c2
OpenEye OEToolkits 2.0.7CNC(=O)c1ccccc1Sc2ccc3c(c2)[nH]nc3C=Cc4ccccn4
FormulaC22 H18 N4 O S
NameAXITINIB;
N-METHYL-2-(3-((E)-2-PYRIDIN-2-YL-VINYL)-1H-INDAZOL-6-YLSULFANYL)-BENZAMIDE
ChEMBLCHEMBL1289926
DrugBankDB06626
ZINCZINC000003816287
PDB chain4agc Chain A Residue 2000 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4agc Molecular Conformations, Interactions, and Properties Associated with Drug Efficiency and Clinical Performance Among Vegfr Tk Inhibitors.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		V848 A866 K868 E885 V914 V916 E917 F918 C919 K920 G922 L1035 C1045 D1046 F1047 A1168
Binding residue
(residue number reindexed from 1)		V41 A59 K61 E78 V107 V109 E110 F111 C112 K113 G115 L171 C181 D182 F183 A304
Annotation score1
Binding affinityMOAD: Ki=0.02nM
PDBbind-CN: -logKd/Ki=10.70,Ki=0.020nM
Enzymatic activity
Catalytic site (original residue number in PDB) D1028 A1030 R1032 N1033 D1046 D1064
Catalytic site (residue number reindexed from 1) D164 A166 R168 N169 D182 D200
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

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Molecular Function
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Biological Process
External links
PDB RCSB:4agc, PDBe:4agc, PDBj:4agc
PDBsum4agc
PubMed22988103
UniProtP35968|VGFR2_HUMAN Vascular endothelial growth factor receptor 2 (Gene Name=KDR)

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