SMTL ID : 7sdc.1

Structure of the SARS-CoV-2 main protease in complex with inhibitor MI-09

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

2 x I80: (1R,2S,5S)-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-{[4-(trifluoromethoxy)phenoxy]acetyl}-3-azabicyclo[3.1.0]hexane-2-carboxamide(Covalent)

I80.1: 19 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, P.168, H.172, D.187, R.188, Q.189, T.190, A.191 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:H.41, A:M.165, A:Q.189 Hydrogen bonds: A:G.143, A:C.145, A:H.164, A:E.166, A:E.166 pi-Stacking: A:H.41 I80.2: 19 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, P.168, H.172, D.187, R.188, Q.189, T.190, A.191 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:H.41, B:M.165, B:Q.189 Hydrogen bonds: B:G.143, B:C.145, B:H.164, B:E.166, B:E.166 pi-Stacking: B:H.41

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Geng, Z.Z. et al., A Systematic Survey of Reversibly Covalent Dipeptidyl Inhibitors of the SARS-CoV-2 Main Protease. J.Med.Chem. (2023)

Release Date

2022-11-09

Peptides

3C-like proteinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

3C-like proteinase

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