Discovery of novel cyanamide-based inhibitors of cathepsin C

Structure

x-ray diffraction · 1 distinct chain · 19% helix, 36% strand (DSSP).

Ligands and binding sites

• LXV · 2,5-dibromo-N-{(3R,5S)-1-[(Z)-iminomethyl]-5-methylpyrrolidin-3-yl}benzenesulfonamide · ligand · chains A
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
• CL · Chloride ion · ion · 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, 1 with a druggability of 0.5 or more.

Modifications

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

Compared structures

• 3PDF · Discovery of Novel Cyanamide-Based Inhibitors of Cathepsin C · 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 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 P53634
• Elsewhere: RCSB PDB 3PDF · PDBe 3PDF · UniProt P53634