Crystal structures of recombinant rat cathepsin B and a cathepsin B- inhibitor complex: implications for structure-based inhibitor design

Structure

x-ray diffraction · 1 distinct chain · 25% helix, 25% strand (DSSP).

Ligands and binding sites

• 0E6 · amino{[(4S)-4-{[(benzyloxy)carbonyl]amino}-5-{[(2S)-1-(benzyloxy)-4-chloro-3-oxobutan-2-yl]amino}-5-oxopentyl]amino}met haniminium · ligand · 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 · 788 Ų buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide, 2 covalent (disulfide, covalent ligand).

Compared structures

• 1THE · Crystal structures of recombinant rat cathepsin B and a cathepsin B-inhibitor complex… · the same entry in another collection · chain B against B, TM-score 1.00
• P00787 · AlphaFold monomer V2.0 prediction for cathepsin B (P00787) · a predicted model of the same protein · chain B 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 P00787
• Elsewhere: RCSB PDB 1THE · PDBe 1THE · UniProt P00787