Structure of PDB 3wzd Chain A Binding Site BS01

Receptor Information
>3wzd Chain A (length=278) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LPYDASKWEFPRDRLKLGKPLGGQVIEADAFGIDKTATCRTVAVKMLKEG
ATHSEHRALMSELKILIHIGHHLNVVNLLGACTKPGGPLMVIVEFCKFGN
LSTYLRSKRNEFVPYKVAPEDLYKDFLTLEHLICYSFQVAKGMEFLASRK
CIHRDLAARNILLSEKNVVKICDFGLALPLKWMAPETIFDRVYTIQSDVW
SFGVLLWEIFSLGASPYPGVKIDEEFCRRLKEGTRMRAPDYTTPEMYQTM
LDCWHGEPSQRPTFSELVEHLGNLLQAN
Ligand information
Ligand IDLEV
InChIInChI=1S/C21H19ClN4O4/c1-29-19-10-17-13(9-14(19)20(23)27)18(6-7-24-17)30-12-4-5-16(15(22)8-12)26-21(28)25-11-2-3-11/h4-11H,2-3H2,1H3,(H2,23,27)(H2,25,26,28)
InChIKeyWOSKHXYHFSIKNG-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385COc1cc2nccc(Oc3ccc(NC(=O)NC4CC4)c(Cl)c3)c2cc1C(N)=O
OpenEye OEToolkits 1.7.6COc1cc2c(cc1C(=O)N)c(ccn2)Oc3ccc(c(c3)Cl)NC(=O)NC4CC4
ACDLabs 12.01COc2cc1nccc(c1cc2C(N)=O)Oc3cc(c(cc3)NC(=O)NC4CC4)Cl
FormulaC21 H19 Cl N4 O4
Name4-{3-chloro-4-[(cyclopropylcarbamoyl)amino]phenoxy}-7-methoxyquinoline-6-carboxamide;
lenvatinib
ChEMBLCHEMBL1289601
DrugBankDB09078
ZINCZINC000003816292
PDB chain3wzd 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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PDB3wzd Distinct binding mode of multikinase inhibitor lenvatinib revealed by biochemical characterization.
Resolution1.57 Å
Binding residue
(original residue number in PDB)		L840 G841 A866 E885 V916 F918 C919 L1035 C1045 D1046 F1047
Binding residue
(residue number reindexed from 1)		L21 G22 A43 E62 V93 F95 C96 L162 C172 D173 F174
Annotation score1
Binding affinityMOAD: Kd=2.1nM
BindingDB: IC50=4nM,Kd=2.1nM
Enzymatic activity
Catalytic site (original residue number in PDB) D1028 A1030 R1032 N1033 D1046
Catalytic site (residue number reindexed from 1) D155 A157 R159 N160 D173
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:3wzd, PDBe:3wzd, PDBj:3wzd
PDBsum3wzd
PubMed25589937
UniProtP35968|VGFR2_HUMAN Vascular endothelial growth factor receptor 2 (Gene Name=KDR)

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