Structure of PDB 3wze Chain A Binding Site BS01

Receptor Information
>3wze Chain A (length=298) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EHCERLPYDASKWEFPRDRLKLGKPLGRGAFGQVIEADAFGIDKTATCRT
VAVKMLKEGATHSEHRALMSELKILIHIGHHLNVVNLLGACTKPGGPLMV
IVEFCKFGNLSTYLRSKRNEFVPYKDLYKDFLTLEHLICYSFQVAKGMEF
LASRKCIHRDLAARNILLSEKNVVKICDFGLARDIYKDPDYVRKGARLPL
KWMAPETIFDRVYTIQSDVWSFGVLLWEIFSLGASPYPGVKIDEEFCRRL
KEGTRMRAPDYTTPEMYQTMLDCWHGEPSQRPTFSELVEHLGNLLQAN
Ligand information
Ligand IDBAX
InChIInChI=1S/C21H16ClF3N4O3/c1-26-19(30)18-11-15(8-9-27-18)32-14-5-2-12(3-6-14)28-20(31)29-13-4-7-17(22)16(10-13)21(23,24)25/h2-11H,1H3,(H,26,30)(H2,28,29,31)
InChIKeyMLDQJTXFUGDVEO-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C(c3nccc(Oc2ccc(NC(=O)Nc1ccc(Cl)c(c1)C(F)(F)F)cc2)c3)NC
OpenEye OEToolkits 1.5.0CNC(=O)c1cc(ccn1)Oc2ccc(cc2)NC(=O)Nc3ccc(c(c3)C(F)(F)F)Cl
CACTVS 3.341CNC(=O)c1cc(Oc2ccc(NC(=O)Nc3ccc(Cl)c(c3)C(F)(F)F)cc2)ccn1
FormulaC21 H16 Cl F3 N4 O3
Name4-{4-[({[4-CHLORO-3-(TRIFLUOROMETHYL)PHENYL]AMINO}CARBONYL)AMINO]PHENOXY}-N-METHYLPYRIDINE-2-CARBOXAMIDE;
Sorafenib
ChEMBLCHEMBL1336
DrugBankDB00398
ZINCZINC000001493878
PDB chain3wze Chain A Residue 1201 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3wze Distinct binding mode of multikinase inhibitor lenvatinib revealed by biochemical characterization.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		V848 A866 E885 V916 F918 C919 G922 H1026 L1035 I1044 C1045 D1046 F1047
Binding residue
(residue number reindexed from 1)		V34 A52 E71 V102 F104 C105 G108 H158 L167 I176 C177 D178 F179
Annotation score1
Binding affinityMOAD: Kd=33nM
BindingDB: IC50=90nM,Kd=59nM,Ki=22nM,EC50=500nM
Enzymatic activity
Catalytic site (original residue number in PDB) D1028 A1030 R1032 N1033 D1046 K1055
Catalytic site (residue number reindexed from 1) D160 A162 R164 N165 D178 K187
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:3wze, PDBe:3wze, PDBj:3wze
PDBsum3wze
PubMed25589937
UniProtP35968|VGFR2_HUMAN Vascular endothelial growth factor receptor 2 (Gene Name=KDR)

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