SMTL ID : 9el4.1

Crystal Structure of SARS-CoV-2 Mpro mutant E166A with Pfizer Intravenous Inhibitor PF-00835231

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

homo-dimer

Ligands

3 x GOL: GLYCEROL

GOL.1: 3 residues within 4Å: Chain A: R.105, N.180, F.181 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.105, A:N.180 Water bridges: A:R.105, A:E.178, A:E.178, A:F.181, A:F.181, A:G.183 GOL.3: 3 residues within 4Å: Chain A: V.166, Q.189 Ligands: V2M.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.189 GOL.4: 9 residues within 4Å: Chain A: M.6, A.7, F.8, S.113, Q.127, D.295, R.298 Chain B: S.123, G.124 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:M.6, A:Q.127, A:R.298 Water bridges: A:D.295

2 x V2M: N-[(2S)-1-({(2S,3S)-3,4-dihydroxy-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide

V2M.2: 23 residues within 4Å: Chain A: L.27, H.41, M.49, Y.54, F.140, L.141, N.142, G.143, S.144, C.145, H.163, H.164, M.165, V.166, L.167, P.168, H.172, D.187, R.188, Q.189, T.190, A.191 Ligands: GOL.3 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:V.166, A:P.168, A:D.187, A:A.191 Hydrogen bonds: A:F.140, A:G.143, A:S.144, A:S.144, A:C.145, A:H.164, A:V.166, A:V.166, A:Q.189 Water bridges: A:N.142, A:Q.189 V2M.5: 23 residues within 4Å: Chain A: S.1 Chain B: L.27, H.41, M.49, Y.54, F.140, L.141, N.142, G.143, S.144, C.145, H.163, H.164, M.165, V.166, L.167, P.168, H.172, D.187, R.188, Q.189, T.190, A.191 16 PLIP interactions: 15 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:M.49, B:V.166, B:D.187, B:A.191 Hydrogen bonds: B:F.140, B:G.143, B:S.144, B:S.144, B:C.145, B:H.164, B:V.166, B:V.166, B:Q.189, A:S.1 Water bridges: B:Q.189, B:Q.189

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zvornicanin, S.N. et al., Molecular mechanisms of drug resistance and compensation in SARS-CoV-2 main protease: the interplay between E166 and L50. Mbio (2025)

Release Date

2025-03-19

Peptides

3C-like proteinase nsp5: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

3C-like proteinase nsp5

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