3WZD image
Entry Detail
PDB ID:
3WZD
Title:
KDR in complex with ligand lenvatinib
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2014-09-24
Release Date:
2015-05-27
Method Details:
Experimental Method:
Resolution:
1.57 Å
R-Value Free:
0.21
R-Value Work:
0.18
R-Value Observed:
0.18
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Vascular endothelial growth factor receptor 2
Mutations:T940V
Chain IDs:A
Chain Length:309
Number of Molecules:1
Biological Source:Homo sapiens
Primary Citation
Distinct binding mode of multikinase inhibitor lenvatinib revealed by biochemical characterization.
ACS MED.CHEM.LETT. 6 89 94 (2015)
PMID: 25589937 DOI: 10.1021/ml500394m

Abstact

Lenvatinib is an oral multikinase inhibitor that selectively inhibits vascular endothelial growth factor (VEGF) receptors 1 to 3 and other proangiogenic and oncogenic pathway-related receptor tyrosine kinases. To elucidate the origin of the potency of lenvatinib in VEGF receptor 2 (VEGFR2) inhibition, we conducted a kinetic interaction analysis of lenvatinib with VEGFR2 and X-ray analysis of the crystal structure of VEGFR2-lenvatinib complexes. Kinetic analysis revealed that lenvatinib had a rapid association rate constant and a relatively slow dissociation rate constant in complex with VEGFR2. Co-crystal structure analysis demonstrated that lenvatinib binds at its ATP mimetic quinoline moiety to the ATP binding site and to the neighboring region via a cyclopropane ring, adopting an Asp-Phe-Gly (DFG)-"in" conformation. These results suggest that lenvatinib is very distinct in its binding mode of interaction compared to the several approved VEGFR2 kinase inhibitors.

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Primary Citation of related structures