7VTH

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.208 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

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This is version 1.3 of the entry. See complete history


Literature

Discovery of S-217622, a Noncovalent Oral SARS-CoV-2 3CL Protease Inhibitor Clinical Candidate for Treating COVID-19.

Unoh, Y.Uehara, S.Nakahara, K.Nobori, H.Yamatsu, Y.Yamamoto, S.Maruyama, Y.Taoda, Y.Kasamatsu, K.Suto, T.Kouki, K.Nakahashi, A.Kawashima, S.Sanaki, T.Toba, S.Uemura, K.Mizutare, T.Ando, S.Sasaki, M.Orba, Y.Sawa, H.Sato, A.Sato, T.Kato, T.Tachibana, Y.

(2022) J Med Chem 65: 6499-6512

  • DOI: https://doi.org/10.1021/acs.jmedchem.2c00117
  • Primary Citation of Related Structures:  
    7VTH, 7VU6

  • PubMed Abstract: 

    The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has resulted in millions of deaths and threatens public health and safety. Despite the rapid global spread of COVID-19 vaccines, effective oral antiviral drugs are urgently needed. Here, we describe the discovery of S-217622 , the first oral noncovalent, nonpeptidic SARS-CoV-2 3CL protease inhibitor clinical candidate. S-217622 was discovered via virtual screening followed by biological screening of an in-house compound library, and optimization of the hit compound using a structure-based drug design strategy. S-217622 exhibited antiviral activity in vitro against current outbreaking SARS-CoV-2 variants and showed favorable pharmacokinetic profiles in vivo for once-daily oral dosing. Furthermore, S-217622 dose-dependently inhibited intrapulmonary replication of SARS-CoV-2 in mice, indicating that this novel noncovalent inhibitor could be a potential oral agent for treating COVID-19.


  • Organizational Affiliation

    Shionogi Pharmaceutical Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-like proteinase
A, B
311Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
EC: 3.4.22.69
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTD1 
Go to UniProtKB:  P0DTD1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTD1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
7XB (Subject of Investigation/LOI)
Query on 7XB

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
2-[4-[[4-[bis(fluoranyl)methoxy]-2-methyl-phenyl]amino]-2,6-bis(oxidanylidene)-3-[[3,4,5-tris(fluoranyl)phenyl]methyl]-1,3,5-triazin-1-yl]-N-methyl-ethanamide
C21 H18 F5 N5 O4
JHDIUUFGPILEJO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.208 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.411α = 90
b = 54.27β = 99.42
c = 114.497γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction
CrysalisProdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 7XBClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-06
    Type: Initial release
  • Version 1.1: 2022-04-13
    Changes: Database references
  • Version 1.2: 2022-05-25
    Changes: Database references
  • Version 1.3: 2023-11-29
    Changes: Data collection, Refinement description