SMTL ID : 9kr5.1

Crystal structure of SARS-CoV-2 main protease in complex with compound 3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

homo-dimer

Ligands

2 x 01: (6~{E})-6-(6-chloranyl-2-methyl-indazol-5-yl)imino-3-[5-[(3~{S})-oxolan-3-yl]oxypyridin-3-yl]-1-[[2,4,5-tris(fluoranyl)phenyl]methyl]-1,3,5-triazinane-2,4-dione

01.1: 21 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 Chain B: S.1 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:T.25, A:M.165 Hydrogen bonds: A:T.24, A:T.26, A:G.143, A:S.144, A:S.144, A:E.166, B:S.1 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, 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: 9 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:T.25, B:M.165 Hydrogen bonds: B:T.24, B:T.26, B:G.143, B:S.144, B:S.144, B:E.166, A:S.1 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

Related Entries With Identical Sequence