Crystal structure of SARS-cov-2 main protease in complex with an inhibitor tkb-198

Structure

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

Ligands and binding sites

• T1X · 7-fluoro-N-[(2S)-1-({(1S,2S)-1-(4-fluoro-1,3-benzothiazol-2-yl)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide · ligand · 2 copies · chains A, B
• DMS · Dimethyl sulfoxide · additive · 2 copies · chains A, B
• 1PE · Pentaethylene glycol · additive · chains A
• MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A
• PG0 · 2-(2-methoxyethoxy)ethanol · additive · chains A, B

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

Pockets

7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 1276 Ų buried · 33 hydrogen bonds · protein-protein

Modifications

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

Compared structures

• 8DOY · Crystal structure of SARS-CoV-2 main protease in complex with an inhibitor TKB-198 · 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 8DOY · PDBe 8DOY · UniProt P0DTD1