› 6xvk

X-ray diffraction
1.99Å resolution

Crystal structure of the KDR (VEGFR2) kinase domain in complex with a type-II inhibitor bearing an acrylamide

Released:
DOI: 10.2210/pdb6xvk/pdb
PDB entry 6xvk coloured by chain, front view.
PDB entry 6xvk coloured by chain, side view.
PDB entry 6xvk coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Alkynyl Benzoxazines and Dihydroquinazolines as Cysteine Targeting Covalent Warheads and Their Application in Identification of Selective Irreversible Kinase Inhibitors.
McAulay K, Hoyt EA, Thomas M, Schimpl M, Bodnarchuk MS, Lewis HJ, Barratt D, Bhavsar D, Robinson DM, Deery MJ, Ogg DJ, Bernardes GJL, Ward RA, Waring MJ, Kettle JG
J Am Chem Soc 142 10358-10372 (2020)
PMID: 32412754

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: 322 amino acids
Theoretical weight: 36.99 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P35968 (Residues: 806-1171; Coverage: 24%)
Gene names: FLK1, KDR, VEGFR2
Sequence domains: Protein tyrosine and serine/threonine kinase

Ligands and Environments

1 bound ligand:
Ligand O3E 1 x O3E
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SOLEIL BEAMLINE PROXIMA 2
Spacegroup: P21
Unit cell:
a: 51.55Å b: 57.01Å c: 59.89Å
α: 90° β: 109.73° γ: 90°
R-values:
R R work R free
0.208 0.206 0.244
Expression system: Spodoptera frugiperda

Quick links

Citations

4 review citations

Covalent Warheads Targeting Cysteine Residue: The Promising Approach in Drug Development.
Huang et al. (2022)
3 more

1 mention without citation

Exploring the mechanism of Dahuang-Tusizi drug pair in the treatment of diabetes nephropathy based on network pharmacology and immune infiltration analysis.
Liu et al. (2023)