Crystal structure of the kinase domain of human C-kit in complex with a type-II inhibitor bearing an acrylamide

Structure

x-ray diffraction · 2 distinct chains · 42% helix, 18% strand (DSSP).

Ligands and binding sites

• O2K · ~{N}-[[3-[2-[3-methoxy-5-(7-methoxyquinolin-4-yl)oxy-pyridin-2-yl]ethanoylamino]-5-methyl-phenyl]methyl]propanamide · 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 · 853 Ų buried · 9 hydrogen bonds · protein-protein

Compared structures

• 6XVA · Crystal structure of the kinase domain of human c-KIT in complex with a type-II 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 A 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 6XVA · PDBe 6XVA · UniProt P10721