› 3wzd

X-ray diffraction
1.57Å resolution

KDR in complex with ligand lenvatinib

Released:
DOI: 10.2210/pdb3wzd/pdb
PDB entry 3wzd coloured by chain, front view.
PDB entry 3wzd coloured by chain, side view.
PDB entry 3wzd coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Distinct binding mode of multikinase inhibitor lenvatinib revealed by biochemical characterization.
Okamoto K, Ikemori-Kawada M, Jestel A, von König K, Funahashi Y, Matsushima T, Tsuruoka A, Inoue A, Matsui J
ACS Med Chem Lett 6 89-94 (2015)
PMID: 25589937

Function and Biology Details

Reaction catalysed: 
ATP + a [protein]-L-tyrosine = ADP + a [protein]-L-tyrosine phosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-153084 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Vascular endothelial growth factor receptor 2 Chain: A
Molecule details ›
Chain: A
Length: 309 amino acids
Theoretical weight: 35.34 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P35968 (Residues: 814-1172; Coverage: 23%)
Gene names: FLK1, KDR, VEGFR2
Sequence domains: Protein tyrosine and serine/threonine kinase
Structure domains:

Ligands and Environments

5 bound ligands:
Ligand LEV 1 x LEV
Ligand DTT 4 x DTT
Ligand EDO 4 x EDO
Ligand GOL 1 x GOL
Ligand SO4 1 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P21
Unit cell:
a: 42.334Å b: 84.225Å c: 46.892Å
α: 90° β: 100.2° γ: 90°
R-values:
R R work R free
0.184 0.181 0.212
Expression system: Spodoptera frugiperda

Quick links

Citations

27 review citations

FDA-approved small-molecule kinase inhibitors.
Wu et al. (2015)
26 more

21 mentions without citation

Quinoline-Based Molecules Targeting c-Met, EGF, and VEGF Receptors and the Proteins Involved in Related Carcinogenic Pathways.
Martorana et al. (2020)
20 more