SMTL ID : 9ksk.1

Crystal structure of SARS-CoV-2 main protease in complex with compound 10

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

homo-dimer

Ligands

2 x 01: 4-[4-chloranyl-2-[[(6E)-6-(6-chloranyl-2-methyl-indazol-5-yl)imino-3-(5-methylpyridin-3-yl)-2,4-bis(oxidanylidene)-1,3,5-triazinan-1-yl]methyl]-5-fluoranyl-phenoxy]-2-fluoranyl-benzenecarbonitrile

01.1: 26 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, L.167, P.168, H.172, D.187, R.188, Q.189, T.190, A.191, Q.192 Chain B: S.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:T.25, A:M.165, A:Q.189 Hydrogen bonds: A:T.26, A:G.143, A:S.144, A:C.145, A:E.166, A:Q.189, A:Q.192 Water bridges: A:N.142 pi-Stacking: A:H.41 01.2: 25 residues within 4Å: Chain A: S.1 Chain B: T.24, T.25, T.26, 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, A.191, Q.192 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:T.25, B:M.165, B:E.166, B:Q.189 Hydrogen bonds: B:T.26, B:L.141, B:G.143, B:S.144, B:C.145, B:E.166, B:Q.192 Water bridges: B:N.142 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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

3C-like proteinase

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