N-terminal finger stabilizes feline drug GC376 in coronavirus 3CL protease

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.195 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


N-Terminal Finger Stabilizes the S1 Pocket for the Reversible Feline Drug GC376 in the SARS-CoV-2 M pro Dimer.

Arutyunova, E.Khan, M.B.Fischer, C.Lu, J.Lamer, T.Vuong, W.van Belkum, M.J.McKay, R.T.Tyrrell, D.L.Vederas, J.C.Young, H.S.Lemieux, M.J.

(2021) J Mol Biol 433: 167003-167003

  • DOI: https://doi.org/10.1016/j.jmb.2021.167003
  • Primary Citation of Related Structures:  
    7LCP, 7LCQ

  • PubMed Abstract: 

    The main protease (M pro , also known as 3CL protease) of SARS-CoV-2 is a high priority drug target in the development of antivirals to combat COVID-19 infections. A feline coronavirus antiviral drug, GC376, has been shown to be effective in inhibiting the SARS-CoV-2 main protease and live virus growth. As this drug moves into clinical trials, further characterization of GC376 with the main protease of coronaviruses is required to gain insight into the drug's properties, such as reversibility and broad specificity. Reversibility is an important factor for therapeutic proteolytic inhibitors to prevent toxicity due to off-target effects. Here we demonstrate that GC376 has nanomolar K i values with the M pro from both SARS-CoV-2 and SARS-CoV strains. Restoring enzymatic activity after inhibition by GC376 demonstrates reversible binding with both proteases. In addition, the stability and thermodynamic parameters of both proteases were studied to shed light on physical chemical properties of these viral enzymes, revealing higher stability for SARS-CoV-2 M pro . The comparison of a new X-ray crystal structure of M pro from SARS-CoV complexed with GC376 reveals similar molecular mechanism of inhibition compared to SARS-CoV-2 M pro , and gives insight into the broad specificity properties of this drug. In both structures, we observe domain swapping of the N-termini in the dimer of the M pro , which facilitates coordination of the drug's P1 position. These results validate that GC376 is a drug with an off-rate suitable for clinical trials.

  • Organizational Affiliation

    Department of Biochemistry, Faculty of Medicine and Dentistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton T6G 2R3, Alberta, Canada; Li Ka Shing Institute of Virology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton T6G 2E1, Alberta, Canada.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-like proteinase306Severe acute respiratory syndrome-related coronavirusMutation(s): 0 
Gene Names: rep1a-1b
Find proteins for P0C6X7 (Severe acute respiratory syndrome coronavirus)
Explore P0C6X7 
Go to UniProtKB:  P0C6X7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C6X7
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.195 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.28α = 90
b = 82.19β = 104.338
c = 54.06γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)Canada--
Natural Sciences and Engineering Research Council (NSERC, Canada)Canada549297-2019

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-12
    Type: Initial release
  • Version 1.1: 2021-05-19
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Advisory, Data collection, Database references, Refinement description, Structure summary