SMTL ID : 9vs1.1

Crystal structure of SARS-CoV-2 3CL protease in complex with compound 15

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x 01: 4-chloranyl-3-[6-methyl-3-[(1-methyl-1,2,4-triazol-3-yl)methyl]-2,4,5-tris(oxidanylidene)-1-[[3,4,5-tris(fluoranyl)phenyl]methyl]pyrido[4,3-d]pyrimidin-7-yl]benzenecarbonitrile

01.1: 22 residues within 4Å: Chain A: T.27, T.28, L.29, H.43, V.44, C.46, S.48, M.51, F.142, L.143, N.144, G.145, S.146, C.147, H.165, H.166, M.167, E.168, H.174, D.189, R.190, Q.191 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:T.27, A:M.167 Hydrogen bonds: A:G.145, A:S.146, A:S.146, A:C.147, A:E.168, A:E.168 Water bridges: A:S.48 pi-Stacking: A:H.43 01.3: 23 residues within 4Å: Chain A: S.3 Chain B: T.27, T.28, L.29, H.43, V.44, C.46, S.48, M.51, F.142, L.143, N.144, G.145, S.146, C.147, H.165, H.166, M.167, E.168, D.189, R.190, Q.191 Ligands: EDO.4 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:T.27, B:M.167 Hydrogen bonds: B:G.145, B:S.146, B:S.146, B:C.147, B:E.168 Water bridges: B:S.48, B:E.168 pi-Stacking: B:H.43

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

EDO.2: 9 residues within 4Å: Chain A: M.167, E.168, L.169, P.170, R.190, Q.191, T.192, A.193, Q.194 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.191, A:T.192, A:Q.194 EDO.4: 9 residues within 4Å: Chain B: M.167, E.168, L.169, P.170, R.190, Q.191, T.192, Q.194 Ligands: 01.3 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.168, B:R.190, B:T.192, B:Q.194

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Taoda, Y. et al., Design, synthesis and biological evaluation of novel quinazolinedione derivatives as non-covalent SARS-CoV-2 3CL protease inhibitors. Bioorg.Med.Chem.Lett. (2025)

Release Date

2025-09-24

Peptides

3C-like proteinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

3C-like proteinase

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