SMTL ID : 9mei.1

Crystal Structure of SARS-CoV-2 Mpro mutant L50F E166V with Pfizer Intravenous Inhibitor PF-00835231

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.84 Å

Oligo State

homo-dimer

Ligands

1 x DMS: DIMETHYL SULFOXIDE

DMS.1: 2 residues within 4Å: Chain A: Q.189 Ligands: V2M.2 No protein-ligand interaction detected (PLIP)

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: 25 residues within 4Å: Chain A: L.27, H.41, M.49, F.50, 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, V.186, D.187, R.188, Q.189, T.190, A.191 Ligands: DMS.1 13 PLIP interactions: 13 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:C.145, A:H.164, A:V.166, A:V.166, A:Q.189 Water bridges: A:Q.189 V2M.3: 24 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 Ligands: CL.4 12 PLIP interactions: 10 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:A.191 Hydrogen bonds: 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, A:S.1 Water bridges: B:Q.189

1 x CL: CHLORIDE ION

CL.4: 1 residues within 4Å: Ligands: V2M.3 Ligand excluded by PLIP

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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