SMTL ID : 9ksj.1

Crystal structure of SARS-CoV-2 main protease in complex with compound 8

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.67 Å

Oligo State

homo-dimer

Ligands

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

01.1: 21 residues within 4Å: Chain A: T.24, T.25, T.26, L.27, P.39, H.41, 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 Chain B: S.1 14 PLIP interactions: 1 interactions with chain B, 13 interactions with chain A Hydrogen bonds: B:S.1, A:T.26, A:L.141, A:G.143, A:H.164, A:E.166 Hydrophobic interactions: A:T.25, A:H.41, A:D.187, A:Q.189 Water bridges: A:H.41, A:N.142, A:C.145 pi-Stacking: A:H.41 01.2: 21 residues within 4Å: Chain A: S.1 Chain B: T.24, T.25, T.26, L.27, P.39, H.41, 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 14 PLIP interactions: 13 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:T.25, B:H.41, B:D.187, B:Q.189 Hydrogen bonds: B:T.26, B:L.141, B:G.143, B:H.164, B:E.166, A:S.1 Water bridges: B:H.41, B:N.142, B:C.145 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