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

Structure

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

Ligands and binding sites

• Y8S · (1R,2S)-2-((S)-2-(((((1R,3S,5S)-bicyclo[3.3.1]non-6-en-3-yl)methoxy)carbonyl)amino)-4-methylpentanamido)-1-hydroxy-3-((S)-2-oxopyrrolidin-3-yl)propane-1-sulfonic acid · ligand · 2 copies · chains A, B
• Y8V · (1S,2S)-2-((S)-2-(((((1R,3S,5S)-bicyclo[3.3.1]non-6-en-3-yl)methoxy)carbonyl)amino)-4-methylpentanamido)-1-hydroxy-3-((S)-2-oxopyrrolidin-3-yl)propane-1-sulfonic acid · ligand · 2 copies · chains A, B
• CL · Chloride ion · ion · chains A
• PO4 · Phosphate ion · ion · 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 · 960 Ų buried · 15 hydrogen bonds · protein-protein

Modifications

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

Compared structures

• 7LKW · 1.65 A resolution structure of SARS-CoV-2 3CL protease in complex with inhibitor 3d… · 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 7LKW · PDBe 7LKW · UniProt P0DTD1