SMTL ID : 7z0p.1

SARS-COV2 Main Protease in complex with inhibitor MG-131

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.52 Å

Oligo State

homo-dimer

Ligands

2 x I8H: (1~{R},2~{S},5~{S})-3-[(2~{S})-2-(~{tert}-butylcarbamoylamino)-3,3-dimethyl-butanoyl]-6,6-dimethyl-~{N}-[(2~{S},3~{R})-4-(methylamino)-3-oxidanyl-4-oxidanylidene-1-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]butan-2-yl]-3-azabicyclo[3.1.0]hexane-2-carboxamide(Covalent)

I8H.1: 20 residues within 4Å: Chain A: H.41, M.49, 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, Q.192 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:H.41, A:E.166, A:L.167, A:Q.192 Hydrogen bonds: A:G.143, A:S.144, A:S.144, A:C.145, A:H.164, A:E.166, A:E.166, A:E.166, A:E.166 I8H.3: 20 residues within 4Å: Chain B: H.41, M.49, 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, Q.192 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:H.41, B:E.166, B:L.167, B:Q.192 Hydrogen bonds: B:G.143, B:S.144, B:S.144, B:C.145, B:H.164, B:E.166, B:E.166, B:E.166, B:E.166

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

NA.2: 5 residues within 4Å: Chain A: R.40, H.41, C.85, H.164, D.187 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.40, A:H.41, A:H.41, A:H.164, A:D.187 NA.4: 5 residues within 4Å: Chain B: R.40, H.41, C.85, H.164, D.187 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.40, B:H.41, B:H.164, B:D.187

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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