SMTL ID : 9ksi.1

Crystal Structure of SARS-CoV-2 main protease in complex with compound 5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x 01: (6E)-1-[[5-chloranyl-4-fluoranyl-2-(4-fluoranylphenoxy)phenyl]methyl]-6-(6-chloranyl-2-methyl-indazol-5-yl)imino-3-(5-methoxypyridin-3-yl)-1,3,5-triazinane-2,4-dione

01.1: 24 residues within 4Å: Chain A: T.24, T.25, T.26, L.27, H.41, 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 Chain B: S.1 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:T.25, A:M.165, A:E.166, A:Q.189 Hydrogen bonds: A:T.26, A:G.143, A:E.166, A:Q.189, B:S.1 Water bridges: A:H.41 pi-Stacking: A:H.41 01.2: 24 residues within 4Å: Chain A: S.1 Chain B: T.24, T.25, T.26, L.27, H.41, 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 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:T.25, B:M.165, B:E.166, B:Q.189 Hydrogen bonds: B:T.26, B:G.143, B:E.166, B:Q.189, A:S.1 Water bridges: B:H.41 pi-Stacking: B:H.41

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, Q. et al., Expanding the utilization of binding pockets proves to be effective for noncovalent small molecule inhibitors against SARS-CoV-2 M pro. Eur.J.Med.Chem. (2025)

Release Date

2025-04-02

Peptides

3C-like proteinase nsp5: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

3C-like proteinase nsp5

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