SMTL ID : 9eet.1

Crystal structure of the SARS-CoV-2 nsp5 main protease (Mpro) E166V mutant in complex with inhibitor GC376

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.39 Å

Oligo State

homo-dimer

Ligands

2 x UED: N~2~-[(benzyloxy)carbonyl]-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide(Covalent)

UED.1: 19 residues within 4Å: Chain A: H.41, Y.54, F.140, L.141, N.142, G.143, S.144, C.145, H.163, H.164, M.165, V.166, P.168, H.172, D.187, R.188, Q.189, T.190 Chain B: S.1 12 PLIP interactions: 9 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:H.41, A:M.165, A:P.168, A:Q.189 Hydrogen bonds: A:G.143, A:S.144, A:C.145, A:H.164, A:V.166, B:S.1, B:S.1 Water bridges: B:S.1 UED.2: 19 residues within 4Å: Chain A: S.1 Chain B: H.41, Y.54, F.140, L.141, N.142, G.143, S.144, C.145, H.163, H.164, M.165, V.166, P.168, H.172, D.187, R.188, Q.189, T.190 12 PLIP interactions: 9 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:H.41, B:M.165, B:P.168, B:Q.189 Hydrogen bonds: B:G.143, B:S.144, B:C.145, B:H.164, B:V.166, A:S.1, A:S.1 Water bridges: A:S.1

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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