Structure of SARS-cov-2 3CL protease in complex with the cyclopropane based inhibitor 17D

Structure

x-ray diffraction · 2 distinct chains · 25% helix, 29% strand (DSSP).

Ligands and binding sites

• PJR · [(1~{S},2~{R})-2-[4,4-bis(fluoranyl) cyclohexyl]cyclopropyl]methyl ~{N}-[(2~{S})-1-[[(1~{S},2~{S})-1-[bis(oxidanyl)-oxidanylidene-$L^{5}-sulfanyl]-1-oxidanyl-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]carbamate · ligand · 2 copies · chains A, B
• P8C · [(1~{S},2~{R})-2-[4,4-bis(fluoranyl) cyclohexyl]cyclopropyl]methyl ~{N}-[(2~{S})-1-[[(1~{R},2~{S})-1-[bis(oxidanyl)-oxidanylidene-$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
• PG4 · Tetraethylene glycol · additive · 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, 4 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 1031 Ų buried · 19 hydrogen bonds · protein-protein

Modifications

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

Compared structures

• 8CZX · Structure of SARS-CoV-2 3CL protease in complex with the cyclopropane based inhibitor 17d · 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 8CZX · PDBe 8CZX · UniProt P0DTD1