Crystal structure of human C-kit kinase domain in complex with a small molecule inhibitor, AZD3229

Structure

x-ray diffraction · 2 distinct chains · 42% helix, 20% strand (DSSP).

Ligands and binding sites

• F8H · ~{N}-[4-[[5-fluoranyl-7-(2-methoxyethoxy)quinazolin-4-yl]amino]phenyl]-2-(4-propan-2-yl-1,2,3-triazol-1-yl) ethanamide · ligand · 2 copies · chains A, B
• CL · Chloride ion · ion · 2 copies · chains A

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 965 Ų buried · 10 hydrogen bonds · protein-protein

Compared structures

• 6GQM · Crystal structure of human c-KIT kinase domain in complex with a small molecule… · 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 6GQM · PDBe 6GQM · UniProt P10721