SMTL ID : 8zt9.1

The Crystal structure of mol066 bound to the main protease (3CLpro/Mpro) of SARS-CoV-2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x 01: 6-[(6-chloranyl-2-propan-2-yl-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: 20 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, H.172, D.187, R.188, Q.189 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:T.25, A:T.26 Hydrogen bonds: A:T.26, A:G.143, 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: 18 residues within 4Å: Chain A: S.1 Chain B: T.24, T.25, T.26, H.41, 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 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:T.25 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, B:Q.189 Salt bridges: B:E.166 pi-Stacking: B:H.41

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain B: R.105, I.106, Q.107, P.108, F.134, Y.182 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.105, B:R.105, B:I.106, B:Q.107 GOL.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: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.123, B:M.6, B:Q.127

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

3C-like proteinase

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