SMTL ID : 9mdq.1

Crystal Structure of SARS-CoV-2 Omicron Main Protease (Mpro) Complex with Azapeptide Inhibitor 20a

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x 01: N-[(2S)-1-{2-(dichloroacetyl)-2-[(2-oxo-1,2-dihydropyridin-3-yl)methyl]hydrazin-1-yl}-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide

01.1: 17 residues within 4Å: Chain A: H.41, F.140, L.141, N.142, G.143, S.144, C.145, H.163, H.164, M.165, E.166, H.172, D.187, R.188, Q.189, T.190, A.191 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:D.187, A:Q.189, A:A.191 Hydrogen bonds: A:G.143, A:S.144, A:S.144, A:C.145, A:H.164, A:E.166, A:E.166, A:E.166, A:Q.189 01.2: 17 residues within 4Å: Chain B: H.41, F.140, L.141, N.142, G.143, S.144, C.145, H.163, H.164, M.165, E.166, H.172, D.187, R.188, Q.189, T.190, A.191 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:D.187, B:Q.189, B:A.191 Hydrogen bonds: B:G.143, B:S.144, B:S.144, B:C.145, B:H.164, B:E.166, B:E.166, B:Q.189

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Flury, P. et al., Azapeptide-Based SARS-CoV-2 Main Protease Inhibitors: Design, Synthesis, Enzyme Inhibition, Structural Determination, and Antiviral Activity. J.Med.Chem. (2025)

Release Date

2025-09-24

Peptides

3C-like proteinase nsp5: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

3C-like proteinase nsp5

Related Entries With Identical Sequence