3WZE

KDR in complex with ligand sorafenib


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.188 

wwPDB Validation 3D Report Full Report



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

  • DOI: 10.1021/ml500394m
  • Structures With Same Primary Citation

  • 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 o ...

    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.


    Organizational Affiliation

    Eisai Co., Ltd , Tsukuba, Ibaraki 300-2635, Japan.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Vascular endothelial growth factor receptor 2
A
309Homo sapiensMutation(s): 1 
Gene Names: KDRFLK1VEGFR2
EC: 2.7.10.1
Find proteins for P35968 (Homo sapiens)
Go to UniProtKB:  P35968
NIH Common Fund Data Resources
PHAROS  P35968
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BAX
Query on BAX

Download CCD File 
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
 Ligand Interaction
DTT
Query on DTT

Download CCD File 
A
2,3-DIHYDROXY-1,4-DITHIOBUTANE
C4 H10 O2 S2
VHJLVAABSRFDPM-IMJSIDKUSA-N
 Ligand Interaction
ACT
Query on ACT

Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BAXKd:  33   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.188 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.921α = 90
b = 57.357β = 94.17
c = 52.17γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-05-27
    Type: Initial release