SMTL ID : 9lvr.1

Crystal structure of SARS-CoV-2 3CL protease in complex with compound 1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x 01: 6-(1,3-dihydroisoindol-2-yl)-3-(5-methylpyridin-3-yl)-1-[[3,4,5-tris(fluoranyl)phenyl]methyl]-1,3,5-triazine-2,4-dione

01.1: 20 residues within 4Å: Chain A: T.48, H.64, C.67, T.68, S.69, M.72, F.163, L.164, N.165, G.166, S.167, C.168, H.186, H.187, M.188, E.189, H.195, D.210, R.211, Q.212 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:T.48, A:M.188, A:E.189 Hydrogen bonds: A:G.166, A:S.167, A:E.189, A:H.195 pi-Stacking: A:H.64 01.3: 20 residues within 4Å: Chain B: T.48, H.64, C.67, T.68, S.69, M.72, F.163, L.164, N.165, G.166, S.167, C.168, H.186, H.187, M.188, E.189, H.195, D.210, R.211, Q.212 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:T.48, B:M.188, B:E.189 Hydrogen bonds: B:G.166, B:E.189 pi-Stacking: B:H.64

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 9 residues within 4Å: Chain A: K.28, V.148, Y.149, Q.150 Chain B: K.28, A.30, V.148, Y.149, Q.150 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.150, B:Q.150

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Unoh, Y. et al., Discovery of The Clinical Candidate S-892216: A Second-Generation of SARS-CoV-2 3CL Protease Inhibitor for Treating COVID-19. To Be Published

Release Date

2025-05-14

Peptides

3C-like proteinase nsp5: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

3C-like proteinase nsp5