SMTL ID : 7z59.1

SARS-CoV-2 main protease (Mpro) covalently modified with a penicillin derivative

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x IFO: (3S)-4-[[2,4-bis(fluoranyl)phenyl]methoxy]-2-methyl-4-oxidanylidene-3-[[(Z)-3-oxidanylidene-2-(2-phenoxyethanoylamino)prop-1-enyl]amino]butane-2-sulfinic acid(Covalent)

IFO.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.164, M.165, E.166, D.187, R.188, Q.189 Chain B: S.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:H.41, A:M.49, A:E.166 Hydrogen bonds: A:H.41, A:G.143, A:S.144, A:C.145, A:E.166 Salt bridges: A:E.166 pi-Stacking: A:H.41 IFO.3: 16 residues within 4Å: Chain A: S.1 Chain B: H.41, M.49, Y.54, F.140, L.141, N.142, G.143, S.144, C.145, H.164, M.165, E.166, D.187, R.188, Q.189 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:H.41, B:M.49, B:E.166 Hydrogen bonds: B:H.41, B:G.143, B:S.144, B:C.145, B:E.166 Salt bridges: B:E.166 pi-Stacking: B:H.41

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 7 residues within 4Å: Chain A: M.6, A.7, F.8, Q.127, R.298 Chain B: S.123, G.124 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.123, A:Q.127, A:R.298 EDO.4: 7 residues within 4Å: Chain A: S.123, G.124 Chain B: M.6, A.7, F.8, Q.127, R.298 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.127, B:R.298, A:S.123

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Malla, T.R. et al., Penicillin Derivatives Inhibit the SARS-CoV-2 Main Protease by Reaction with Its Nucleophilic Cysteine. J.Med.Chem. (2022)

Release Date

2022-06-29

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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