Crystal structure of the kinase domain of human C-kit with a cyclic imidate inhibitor covalently bound to CYS788

Structure

x-ray diffraction · 2 distinct chains · 43% helix, 20% strand (DSSP).

Ligands and binding sites

• O2H · ~{N}-(4,4-dimethyl-2-propyl-3,1-benzoxazin-6-yl)-2-[3-methoxy-5-(7-methoxyquinolin-4-yl)oxy-pyridin-2-yl]ethanamide · ligand · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 1000 Ų buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

• 6XVB · Crystal structure of the kinase domain of human c-KIT with a cyclic imidate inhibitor… · the same entry in another collection · chain A against A, TM-score 1.00
• P10721 · AlphaFold monomer V2.0 prediction for MAST/STEM cell growth factor receptor kit (P10721) · a predicted model of the same protein · chain B against A, TM-score 0.97

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt P10721
• Elsewhere: RCSB PDB 6XVB · PDBe 6XVB · UniProt P10721