3WZE | pdb_00003wze

KDR in complex with ligand sorafenib

• PDB DOI: https://doi.org/10.2210/pdb3WZE/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2014-09-24 Released: 2015-05-27 
• Deposition Author(s): Okamoto, K., Ikemori_Kawada, M., Inoue, A., Matsui, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.224 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Literature

Distinct binding mode of multikinase inhibitor lenvatinib revealed by biochemical characterization.

Okamoto, K., Ikemori-Kawada, M., Jestel, A., von Konig, K., Funahashi, Y., Matsushima, T., Tsuruoka, A., Inoue, A., Matsui, J.

(2015) ACS Med Chem Lett 6: 89-94

• PubMed: 25589937 
• DOI: https://doi.org/10.1021/ml500394m
• Primary Citation Related Structures: 
  3WZD, 3WZE


• PubMed Abstract: 
  

  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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Organizational Affiliation: 
• Eisai Co., Ltd , Tsukuba, Ibaraki 300-2635, Japan.
Proteros Biostructures GmbH , Planegg-Martinsried, Germany.
Eisai, Inc. , 4 Corporate Drive, Andover, Massachusetts 01810, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 36.02 kDa 
• Atom Count: 2,587 
• Modeled Residue Count: 298 
• Deposited Residue Count: 309 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vascular endothelial growth factor receptor 2	A	309	Homo sapiens	Mutation(s): 1  Gene Names: KDR, FLK1, VEGFR2 EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P35968 (Homo sapiens) Explore P35968  Go to UniProtKB:  P35968
PHAROS:  P35968 GTEx:  ENSG00000128052

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BAX	B [auth A]	4-{4-[({[4-CHLORO-3-(TRIFLUOROMETHYL)PHENYL]AMINO}CARBONYL)AMINO]PHENOXY}-N-METHYLPYRIDINE-2-CARBOXAMIDE C21 H16 Cl F3 N4 O3 MLDQJTXFUGDVEO-UHFFFAOYSA-N
DTT	D [auth A]	2,3-DIHYDROXY-1,4-DITHIOBUTANE C4 H10 O2 S2 VHJLVAABSRFDPM-IMJSIDKUSA-N
ACT	C [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
BAX	BindingDB:  3WZE	Ki: min: 0.02, max: 22 (nM) from 3 assay(s)
		Kd: min: 33, max: 93 (nM) from 3 assay(s)
		IC50: min: 0.06, max: 420 (nM) from 60 assay(s)
		EC50: 500 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.224 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.921	α = 90
b = 57.357	β = 94.17
c = 52.17	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-05-27 
Deposition Author(s): Okamoto, K., Ikemori_Kawada, M., Inoue, A., Matsui, J.

Revision History  

• Version 1.0: 2015-05-27
  Type: Initial release
  
• Version 1.1: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Structure summary