Crystal structure of HCV NS3 protease with a boronate inhibitor

Structure

x-ray diffraction · 4 distinct chains · 11% helix, 46% strand (DSSP).

Ligands and binding sites

• BBQ · Cyclopentyl N-[(2S)-1-[(2S,4R)-2-[[(4R)-8-hydroxy-1,6,10-trioxa-5$L^{4}-boraspiro[4.5]decan-4-yl]carbamoyl]-4-isoquinolin-1-yloxy-pyrrolidin-1-yl]-3,3-dimethyl-1-oxo-butan-2-yl]carbamate · ligand · chains A
• ZN · Zinc ion · metal · 2 copies · chains A, B
• MG · Magnesium ion · metal · 2 copies · chains A, C, D

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

6 interfaces between chains.

• A–C · 1302 Ų buried · 30 hydrogen bonds · protein-protein
• B–D · 875 Ų buried · 15 hydrogen bonds · protein-protein
• A–B · 448 Ų buried · 4 hydrogen bonds · protein-protein
• C–D · 323 Ų buried · 5 hydrogen bonds · protein-protein
• A–D · 204 Ų buried · 2 hydrogen bonds · protein-protein

Compared structures

• 2XCF · Crystal structure of HCV NS3 protease with a boronate inhibitor · the same entry in another collection · 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 C1KHN2
• Every structure of UniProt C9WU77
• Elsewhere: RCSB PDB 2XCF · PDBe 2XCF · UniProt C1KHN2 · UniProt C9WU77