Crystal structure of FGFR2 kinase domain gatekeeper mutant V564F in complex with covalent compound 3

Structure

x-ray diffraction · 2 distinct chains · 38% helix, 16% strand (DSSP).

Ligands and binding sites

• WF7 · N-{4-[(E)-2-{4-(4-methylpiperazin-1-yl)-6-[(5-methyl-1H-pyrazol-3-yl)amino]pyrimidin-2-yl}ethenyl]phenyl}prop-2-enamide · ligand · 2 copies · chains A, B
• FLC · Citrate anion · additive · 2 copies · chains A, B
• GOL · Glycerol · additive · 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 · 1346 Ų buried · 17 hydrogen bonds · protein-protein

Modifications

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

Compared structures

• 7KIE · Crystal structure of FGFR2 kinase domain gatekeeper mutant V564F in complex with covalent… · the same entry in another collection · chain A against A, TM-score 1.00
• P21802 · AlphaFold monomer V2.0 prediction for fibroblast growth factor receptor 2 (P21802) · 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 P21802
• Elsewhere: RCSB PDB 7KIE · PDBe 7KIE · UniProt P21802