Protein-ligand complex of a novel macrocyclic HCV NS3 protease inhibitor derived from amino cyclic boronates

Structure

x-ray diffraction · 4 distinct chains · 12% helix, 48% strand (DSSP).

Ligands and binding sites

• TR8 · (1-{[(10-tert-butyl-15,15-dimethyl-3,9,12-trioxo-6,7,9,10,11,12,14,15,16,17,18,19,23,23a-tetradecahydro-1H,5H-2,23:5,8-dimethano-4,13,2,8,11-benzodioxatriazacyclohenicosin-7(3H)-yl)carbonyl]amino}-3-hydroxypropyl)(trihydroxy)borate(1-) · 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, 2 with a druggability of 0.5 or more.

Interfaces

6 interfaces between chains.

• A–C · 1325 Ų buried · 30 hydrogen bonds · protein-protein
• B–D · 856 Ų buried · 15 hydrogen bonds · protein-protein
• A–B · 422 Ų buried · 3 hydrogen bonds · protein-protein
• C–D · 290 Ų buried · 3 hydrogen bonds · protein-protein
• A–D · 201 Ų buried · 2 hydrogen bonds · protein-protein

Modifications

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

Compared structures

• 2XNI · Protein-ligand complex of a novel macrocyclic HCV NS3 protease inhibitor derived from… · 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 C1KHZ7
• Every structure of UniProt C9WU77
• Elsewhere: RCSB PDB 2XNI · PDBe 2XNI · UniProt C1KHZ7 · UniProt C9WU77