SMTL ID : 7tob.1

Crystal structure of the SARS-CoV-2 Omicron main protease (Mpro) in complex with inhibitor GC376

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-dimer

Ligands

2 x K36: (1S,2S)-2-({N-[(benzyloxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid(Covalent)

K36.1: 16 residues within 4Å: Chain A: H.41, M.49, Y.54, 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 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:H.41 Hydrogen bonds: A:G.143, A:S.144, A:C.145, A:H.164, A:E.166, B:S.1 Water bridges: A:N.142, A:N.142 K36.4: 16 residues within 4Å: Chain B: H.41, M.49, Y.54, 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 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:H.41 Hydrogen bonds: B:G.143, B:S.144, B:C.145, B:H.164, B:E.166, B:E.166, A:S.1, A:S.1 Water bridges: B:N.142, B:N.142

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 4 residues within 4Å: Chain A: S.62, N.63, G.79, H.80 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.62, A:N.63, A:H.80, A:H.80 Water bridges: A:H.64 PEG.3: 2 residues within 4Å: Chain A: R.40, N.84 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.40 Water bridges: A:N.84 PEG.5: 4 residues within 4Å: Chain B: S.62, N.63, G.79, H.80 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.62, B:N.63, B:H.80, B:H.80 Water bridges: B:H.64 PEG.6: 2 residues within 4Å: Chain B: R.40, N.84 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.40 Water bridges: B:N.84

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sacco, M.D. et al., The P132H mutation in the main protease of Omicron SARS-CoV-2 decreases thermal stability without compromising catalysis or small-molecule drug inhibition. Cell Res. (2022)

Release Date

2022-02-02

Peptides

3C-like proteinase nsp5: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

3C-like proteinase nsp5

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