Cathepsin-K in complex with miv-701

Structure

x-ray diffraction · 1 distinct chain · 29% helix, 23% strand (DSSP).

Ligands and binding sites

• HFH · ~{N}-[(2~{S})-1-[(3~{R},3~{a}~{R},6~{S},6~{a}~{S})-6-fluoranyl-3-oxidanyl-2,3,3~{a},5,6,6~{a}-hexahydrofuro[3,2-b]pyrrol-4-yl]-4-methyl-1-oxidanylidene-pentan-2-yl]-4-[2-(4-methylpiperazin-1-yl)-1,3-thiazol-4-yl]benzamide · ligand · 2 copies · chains A, B
• MHA · (carbamoylmethyl-carboxymethyl-amino)-acetic acid · ligand · chains B
• NA · Sodium ion · metal · chains A, B
• GOL · Glycerol · additive · chains A

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

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 480 Ų buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide, 2 covalent (disulfide, covalent ligand).

Compared structures

• 6QLM · Cathepsin-K in complex with MIV-701 · 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 1.00

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 6QLM · PDBe 6QLM · UniProt P43235