Structure of human coronavirus NL63 main protease in complex with the alpha-ketoamide tert-butyl ((S)-4-(benzylamino)-3,4-dioxo-1-((S)-2- oxopyrrolidin-3-YL)B- utan-2-YL)CARBAMATE (tert-butyl -glnlactam-co- co-nh-benzyl)

Structure

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

Ligands and binding sites

• 8X8 · ~{tert}-butyl ~{N}-[(2~{S},3~{R})-3-oxidanyl-4-oxidanylidene-1-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]-4-[(phenylmethyl)amino]butan-2-yl]carbamate · ligand · 3 copies · chains A, B, C
• DMS · Dimethyl sulfoxide · additive · 3 copies · chains A, C
• GOL · Glycerol · additive · 2 copies · chains B, C

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

Pockets

10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Interfaces

3 interfaces between chains.

• B–C · 1347 Ų buried · 36 hydrogen bonds · protein-protein
• A–B · 395 Ų buried · 1 hydrogen bond · protein-protein
• A–C · 336 Ų buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 covalent (covalent ligand).

Compared structures

• 5NH0 · Structure of human coronavirus NL63 main protease in complex with the alpha-ketoamide… · 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 P0C6X5
• Elsewhere: RCSB PDB 5NH0 · PDBe 5NH0 · UniProt P0C6X5