HCV NS3 protease domain with ketoamide inhibitor

Structure

x-ray diffraction · 4 distinct chains · 11% helix, 49% strand (DSSP).

Ligands and binding sites

• M66 · (1R,2S,5S)-3-{(2S)-2-(2,3-dihydro-1H-inden-2-yl)-2-[({(1S)-2,2-dimethyl-1-[(2-oxopiperidin-1-yl)methyl]propyl}carbamoyl)amino]acetyl}-6,6-dimethyl-N-{(1S)-1-[oxo(prop-2-en-1-ylamino)acetyl]butyl}-3-azabicyclo[3.1.0]hexane-2-carboxamide · ligand · chains A
• ZN · Zinc ion · metal · 2 copies · chains A, C

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.

Interfaces

6 interfaces between chains.

• A–B · 1308 Ų buried · 27 hydrogen bonds · protein-protein
• C–D · 845 Ų buried · 15 hydrogen bonds · protein-protein
• A–C · 472 Ų buried · 4 hydrogen bonds · protein-protein
• B–D · 283 Ų buried · 5 hydrogen bonds · protein-protein
• B–C · 226 Ų buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

• 3KN2 · HCV NS3 Protease Domain with ketoamide 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 Q9ELS8
• Every structure of UniProt Q9QP61
• Elsewhere: RCSB PDB 3KN2 · PDBe 3KN2 · UniProt Q9ELS8 · UniProt Q9QP61