SMTL ID : 7ql8.1

SARS-COV2 Main Protease in complex with inhibitor MG78

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.81 Å

Oligo State

homo-dimer

Ligands

2 x I70: (1R,2S,5S)-N-{(2S,3R)-4-amino-3-hydroxy-4-oxo-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}-3-[N-(tert-butylcarbamoyl)-3-methyl-L-valyl]-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamide(Covalent)

I70.1: 22 residues within 4Å: Chain A: L.27, H.41, Y.54, F.140, L.141, N.142, G.143, S.144, C.145, H.163, H.164, M.165, E.166, L.167, P.168, H.172, D.187, R.188, Q.189, T.190, A.191, Q.192 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:H.41, A:M.165, A:E.166, A:L.167 Hydrogen bonds: A:G.143, A:S.144, A:C.145, A:H.164, A:E.166, A:E.166, A:E.166, A:E.166, A:E.166 Water bridges: A:N.142 I70.5: 22 residues within 4Å: Chain B: L.27, H.41, Y.54, F.140, L.141, N.142, G.143, S.144, C.145, H.163, H.164, M.165, E.166, L.167, P.168, H.172, D.187, R.188, Q.189, T.190, A.191, Q.192 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:H.41, B:M.165, B:E.166, B:L.167 Hydrogen bonds: B:G.143, B:S.144, B:C.145, B:H.164, B:E.166, B:E.166, B:E.166, B:E.166, B:E.166 Water bridges: B:N.142

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 2 residues within 4Å: Chain A: R.4, K.5 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain B: R.4, K.5 Ligand excluded by PLIP

4 x NA: SODIUM ION(Non-functional Binders)

NA.3: 4 residues within 4Å: Chain A: L.58, I.59, K.61, H.80 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.59 NA.4: 1 residues within 4Å: Chain A: H.80 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.80, A:H.80 NA.7: 4 residues within 4Å: Chain B: L.58, I.59, K.61, H.80 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.61 NA.8: 1 residues within 4Å: Chain B: H.80 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.63, B:H.80

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gohl, M. et al., From Repurposing to Redesign: Optimization of Boceprevir to Highly Potent Inhibitors of the SARS-CoV-2 Main Protease. Molecules (2022)

Release Date

2022-04-27

Peptides

3C-like proteinase nsp5: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
AAA

3C-like proteinase nsp5

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