SMTL ID : 8zuc.1

The Crystal structure of mol080 bound to the main protease (3CLpro/Mpro) of SARS-CoV-2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-1-1-mer

Ligands

2 x 01: 6-[[6-chloranyl-2-(3-methylbutyl)indazol-5-yl]amino]-3-[(1-methyl-1,2,4-triazol-3-yl)methyl]-1-[[2,4,5-tris(fluoranyl)phenyl]methyl]pyrimidine-2,4-dione

01.1: 19 residues within 4Å: Chain A: T.24, T.25, T.26, L.27, H.41, M.49, F.140, L.141, N.142, G.143, S.144, C.145, H.163, H.164, M.165, E.166, D.187, R.188, Q.189 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:T.25, A:T.26, A:M.165 Hydrogen bonds: A:T.26, A:G.143, A:S.144, A:S.144, A:C.145, A:E.166 Water bridges: A:N.142 Salt bridges: A:E.166 pi-Stacking: A:H.41 01.2: 20 residues within 4Å: Chain A: S.1 Chain B: T.24, T.25, T.26, L.27, H.41, M.49, F.140, L.141, N.142, G.143, S.144, C.145, H.163, H.164, M.165, E.166, D.187, R.188, Q.189 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:T.25, B:T.26, B:M.165 Hydrogen bonds: B:T.26, B:G.143, B:S.144, B:S.144, B:C.145, B:E.166 Water bridges: B:N.142 Salt bridges: B:E.166 pi-Stacking: B:H.41

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pan, F. et al., Development of pyrimidone derivatives as nonpeptidic and noncovalent 3-chymotrypsin-like protease (3CL pro ) inhibitors with anti-coronavirus activities. Bioorg.Chem. (2025)

Release Date

2025-06-11

Peptides

3C-like proteinase: A
3C-like proteinase: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

3C-like proteinase

3C-like proteinase

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