SMTL ID : 9eev.1

Crystal structure of the SARS-CoV-2 Omicron nsp5 main protease (Mpro) E166V mutant in complex with inhibitor Nirmatrelvir (PF-07321332)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

2 x 4WI: (1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide(Non-covalent)

4WI.1: 20 residues within 4Å: Chain A: H.41, M.49, Y.54, F.140, L.141, N.142, G.143, C.145, H.163, H.164, M.165, V.166, L.167, P.168, D.187, R.188, Q.189, T.190, Q.192 Chain B: S.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:H.41, A:M.165, A:V.166, A:Q.189 Hydrogen bonds: A:F.140, A:G.143, A:H.164, A:V.166, A:V.166, A:T.190 Halogen bonds: A:V.166, A:Q.192 4WI.2: 20 residues within 4Å: Chain A: S.1 Chain B: H.41, M.49, Y.54, F.140, L.141, N.142, G.143, C.145, H.163, H.164, M.165, V.166, L.167, P.168, D.187, R.188, Q.189, T.190, Q.192 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:H.41, B:M.165, B:V.166, B:Q.189 Hydrogen bonds: B:F.140, B:G.143, B:H.164, B:V.166, B:V.166, B:T.190 Halogen bonds: B:V.166, B:Q.192

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Neilsen, G. et al., Strategy to overcome a nirmatrelvir resistance mechanism in the SARS-CoV-2 nsp5 protease. Sci Adv (2025)

Release Date

2025-06-18

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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