The co-crystal structure of SARS-cov-2 main protease with peptidomimetic inhibitor N-((S)-3-methyl-1-(((S)-4-methyl-1-oxo-1- (((S)-1-oxo-3-((S)-2-oxopiperidin-3-YL)PROPAN-2-YL)AMINO)PENTAN-2- YL)AMINO)-1-oxobutan-2-yl)-4-nitrobenzamide

Structure

x-ray diffraction · 1 distinct chain · 26% helix, 29% strand (DSSP).

Ligands and binding sites

• H6L · ~{N}-[(2~{S})-3-methyl-1-[[(2~{S})-4-methyl-1-oxidanylidene-1-[[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepiperidin-3-yl]propan-2-yl]amino]pentan-2-yl]amino]-1-oxidanylidene-butan-2-yl]-4-nitro-benzamide · 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, 3 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 1471 Ų buried · 41 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

• 7DGI · The co-crystal structure of SARS-CoV-2 main protease with peptidomimetic inhibitor… · 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 P0DTC1
• Elsewhere: RCSB PDB 7DGI · PDBe 7DGI · UniProt P0DTC1