1.65 a resolution structure of SARS-cov 3CL protease in complex with inhibitor 7J

Structure

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

Ligands and binding sites

• VDJ · [4,4-bis(fluoranyl)cyclohexyl]methyl ~{N}-[(2~{S})-1-[[(1~{R},2~{S})-1-[bis(oxidanyl)-oxidanylidene-$l^{5}-sulfanyl]-1-oxidanyl-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]carbamate · ligand · 2 copies · chains A, B
• QYS · (1S,2S)-2-[(N-{[(4,4-difluorocyclohexyl) methoxy]carbonyl}-L-leucyl)amino]-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid · ligand · 2 copies · chains A, 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, 4 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 1307 Ų buried · 28 hydrogen bonds · protein-protein

Modifications

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

Compared structures

• 6W2A · 1.65 A resolution structure of SARS-CoV 3CL protease in complex with inhibitor 7j · 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 P0C6U8
• Elsewhere: RCSB PDB 6W2A · PDBe 6W2A · UniProt P0C6U8