9VS1 | pdb_00009vs1

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.223 (Depositor), 0.225 (DCC) 
  • R-Value Work: 
    0.176 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 
    0.178 (Depositor) 

Starting Model: experimental
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Literature

Design, synthesis and biological evaluation of novel quinazolinedione derivatives as non-covalent SARS-CoV-2 3CL protease inhibitors.

Taoda, Y.Hori, A.Tadano, G.Sugiyama, S.Masakado, S.Tanaka, S.Ogasahara, R.Nakahara, K.Maeno, S.Unoh, Y.Tachibana, Y.Uehara, S.Sako, Y.Yamamoto, S.Kawashima, S.Nobori, H.Kato, T.

(2025) Bioorg Med Chem Lett 129: 130400-130400

  • DOI: https://doi.org/10.1016/j.bmcl.2025.130400
  • Primary Citation of Related Structures:  
    9VS1

  • PubMed Abstract: 

    Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19), has spread around the world since 2020, affecting many people and placing a heavy burden on medical facilities and the economy. The 3C-like protease (3CL pro ) of SARS-CoV-2 is an essential enzyme for viral replication, and has been therefore attracting attention as a drug target. With the aim of creating novel non-covalent 3CL pro inhibitors, we planned a scaffold hopping transformation starting with ensitrelvir, which was discovered by Shionogi. Optimization of the substituents at the 5- and 7-positions of the newly designed quinazolinedione scaffold led to the discovery of compound 16, which exceeds ensitrelvir in enzyme inhibitory and antiviral activities. We solved the X-ray co-crystal structure of our synthesized inhibitor and 3CL pro , and clarified the interaction that contributes to its high activity. The newly discovered compound has shown good results in terms of metabolic stability and oral absorption in rat PK studies. It is expected to be a good lead compound for finding superior 3CL pro inhibitors.


  • Organizational Affiliation
    • Shionogi Pharmaceutical Research Center, Shionogi & Company, Limited, 1-1, Futaba-cho, 3-chome, Toyonaka, Osaka 561-0825, Japan. Electronic address: yoshiyuki.taoda@shionogi.co.jp.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-like proteinase
A, B
308Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
EC: 3.4.22.69
UniProt
Find proteins for P0DTC1 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC1 
Go to UniProtKB:  P0DTC1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTC1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.223 (Depositor), 0.225 (DCC) 
  • R-Value Work:  0.176 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 0.178 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.801α = 90
b = 98.639β = 108.42
c = 59.655γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
CrysalisProdata reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-24
    Type: Initial release