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 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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 


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