1.65 a resolution structure of SARS-cov-2 3CL protease in complex with inhibitor 3B (deuterated analog of inhibitor 2A)

Structure

x-ray diffraction · 2 distinct chains · 26% helix, 29% strand (DSSP).

Ligands and binding sites

• Y4D · (1R,2S)-2-((S)-2-(((((1R,3s,5S)-bicyclo[3.3.1]nonan-3-yl)methoxy)carbonyl)amino)-4-methylpentanamido)-1-hydroxy-3-((S)-2-oxopyrrolidin-3-yl)propane-1-sulfonic acid · ligand · chains A
• Y5S · (1S,2S)-2-((S)-2-(((((1R,3s,5S)-bicyclo[3.3.1]nonan-3-yl)methoxy)carbonyl)amino)-4-methylpentanamido)-1-hydroxy-3-((S)-2-oxopyrrolidin-3-yl)propane-1-sulfonic acid · ligand · chains A
• Y8Y · (1R,2S)-2-((S)-2-(((((1R,3r,5S)-bicyclo[3.3.1]nonan-3-yl)methoxy)carbonyl)amino)-4-methylpentanamido)-1-hydroxy-3-((S)-2-oxopyrrolidin-3-yl)propane-1-sulfonic acid · ligand · chains B
• Y91 · (1S,2S)-2-((S)-2-(((((1R,3r,5S)-bicyclo[3.3.1]nonan-3-yl)methoxy)carbonyl)amino)-4-methylpentanamido)-1-hydroxy-3-((S)-2-oxopyrrolidin-3-yl)propane-1-sulfonic acid · ligand · chains B

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

Pockets

6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 991 Ų buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 covalent (covalent ligand).

Compared structures

• 7LKU · 1.65 A resolution structure of SARS-CoV-2 3CL protease in complex with inhibitor 3b… · 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 P0DTD1
• Elsewhere: RCSB PDB 7LKU · PDBe 7LKU · UniProt P0DTD1