Structure of the activation intermediate of cathepsin K in complex with the azadipeptide nitrile inhibitor GU1303

Structure

x-ray diffraction · 2 distinct chains · 35% helix, 19% strand (DSSP).

Ligands and binding sites

• 9ZG · (phenylmethyl) ~{N}-[(2~{S})-1-[[aminomethyl(methyl) amino]-methyl-amino]-1-oxidanylidene-3-phenyl-propan-2-yl]carbamate · ligand · chains A, P
• MG · Magnesium ion · metal · chains A, P
• CL · Chloride ion · ion · chains A
• EDO · 1,2-ethanediol · additive · 3 copies · chains A, P

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

Pockets

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

Interfaces

1 interface between chains.

• A–P · 890 Ų buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide, 1 covalent (disulfide, covalent ligand).

Compared structures

• 7QBO · Structure of the activation intermediate of cathepsin K in complex with the azadipeptide… · the same entry in another collection · chain A against A, TM-score 1.00
• P43235 · AlphaFold monomer V2.0 prediction for cathepsin K (P43235) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P43235
• Elsewhere: RCSB PDB 7QBO · PDBe 7QBO · UniProt P43235