6-phenyl-1H-IMIDAZO[4,5-C]PYRIDINE-4-carbonitrile as cathepsin S inhibitors

Structure

x-ray diffraction · 2 distinct chains · 29% helix, 23% strand (DSSP).

Ligands and binding sites

• EF3 · (E)-1-(1-methyl-6-{4-[3-(4-methylpiperazin-1-yl)propoxy]-3-(trifluoromethyl)phenyl}-1H-imidazo[4,5-c]pyridin-4-yl)methanimine · ligand · 2 copies · chains A, B
• SO4 · Sulfate ion · ion · chains B
• DMS · Dimethyl sulfoxide · additive · 2 copies · chains A, B

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 757 Ų buried · 10 hydrogen bonds · protein-protein

Modifications

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

Compared structures

• 3N4C · 6-Phenyl-1H-imidazo[4,5-c]pyridine-4-carbonitrile as cathepsin S inhibitors · the same entry in another collection · chain A against A, TM-score 1.00
• P25774 · AlphaFold monomer V2.0 prediction for cathepsin S (P25774) · 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 P25774
• Elsewhere: RCSB PDB 3N4C · PDBe 3N4C · UniProt P25774