Human cathepsin-C in complex with dipeptidyl cyclopropyl nitrile inhibitor 2

Structure

x-ray diffraction · 3 distinct chains · 18% helix, 35% strand (DSSP).

Ligands and binding sites

• HB5 · (2~{S})-2-azanyl-~{N}-[(1~{R},2~{R})-1-(iminomethyl)-2-[4-[4-(4-methylpiperazin-1-yl) sulfonylphenyl]phenyl]cyclopropyl]-3-thiophen-2-yl-propanamide · ligand · chains A, B, C
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, C, B
• MAN · alpha-D-mannopyranose · sugar · 2 copies
• BMA · beta-D-mannopyranose · sugar
• CL · Chloride ion · ion · chains B, C

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

Pockets

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

Interfaces

3 interfaces between chains.

• B–C · 3019 Ų buried · 57 hydrogen bonds · protein-protein
• A–B · 963 Ų buried · 16 hydrogen bonds · protein-protein
• A–C · 341 Ų buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide, 3 glycan, 1 covalent (disulfide, N-glycosylation, covalent ligand).

Compared structures

• 6IC5 · Human cathepsin-C in complex with dipeptidyl cyclopropyl nitrile inhibitor 2 · the same entry in another collection · chain A against A, TM-score 1.00
• P53634 · AlphaFold monomer V2.0 prediction for dipeptidyl peptidase 1 (P53634) · a predicted model of the same protein · chain B 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 P53634
• Elsewhere: RCSB PDB 6IC5 · PDBe 6IC5 · UniProt P53634