Crystal structure (orthorhombic form) of the complex resulting from the reaction between SARS-cov-2 (2019-ncov) main protease and tert- butyl (1-((S)-1-(((S)-4-(benzylamino)-3,4-dioxo-1-((S)-2- oxopyrrolidin-3-YL)BUTAN-2-YL)AMINO)-3-cyclopropyl-1-oxopropan-2-yl)- 2-oxo-1,2-dihydropyridin-3-YL)CARBAMATE (alpha-ketoamide 13B)

Structure

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

Ligands and binding sites

• O6K · ~{tert}-butyl ~{N}-[1-[(2~{S})-3-cyclopropyl-1-oxidanylidene-1-[[(2~{S},3~{R})-3-oxidanyl-4-oxidanylidene-1-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]-4-[(phenylmethyl)amino]butan-2-yl]amino]propan-2-yl]-2-oxidanylidene-pyridin-3-yl]carbamate · ligand · 2 copies · chains A, B
• GLY · Glycine · ligand · chains A, B

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

Pockets

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 1394 Ų buried · 30 hydrogen bonds · protein-protein

Modifications

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

Compared structures

• 6Y2G · Crystal structure (orthorhombic form) of the complex resulting from the reaction between… · 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 6Y2G · PDBe 6Y2G · UniProt P0DTD1