BtSCoV-Rf1.2004 Papain-Like protease bound to the non-covalent inhibitor GRL-0617

Experimental Data Snapshot

  • Resolution: 3.16 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.232 

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Ligand Structure Quality Assessment 

This is version 1.4 of the entry. See complete history


Exploring Noncovalent Protease Inhibitors for the Treatment of Severe Acute Respiratory Syndrome and Severe Acute Respiratory Syndrome-Like Coronaviruses.

Freitas, B.T.Ahiadorme, D.A.Bagul, R.S.Durie, I.A.Ghosh, S.Hill, J.Kramer, N.E.Murray, J.O'Boyle, B.M.Onobun, E.Pirrone, M.G.Shepard, J.D.Enos, S.Subedi, Y.P.Upadhyaya, K.Tripp, R.A.Cummings, B.S.Crich, D.Pegan, S.D.

(2022) ACS Infect Dis 8: 596-611

  • DOI: https://doi.org/10.1021/acsinfecdis.1c00631
  • Primary Citation of Related Structures:  
    7SKQ, 7SKR

  • PubMed Abstract: 

    Over the last 20 years, both severe acute respiratory syndrome coronavirus-1 and severe acute respiratory syndrome coronavirus-2 have transmitted from animal hosts to humans causing zoonotic outbreaks of severe disease. Both viruses originate from a group of betacoronaviruses known as subgroup 2b. The emergence of two dangerous human pathogens from this group along with previous studies illustrating the potential of other subgroup 2b members to transmit to humans has underscored the need for antiviral development against them. Coronaviruses modify the host innate immune response in part through the reversal of ubiquitination and ISGylation with their papain-like protease (PLpro). To identify unique or overarching subgroup 2b structural features or enzymatic biases, the PLpro from a subgroup 2b bat coronavirus, BtSCoV-Rf1.2004, was biochemically and structurally evaluated. This evaluation revealed that PLpros from subgroup 2b coronaviruses have narrow substrate specificity for K48 polyubiquitin and ISG15 originating from certain species. The PLpro of BtSCoV-Rf1.2004 was used as a tool alongside PLpro of CoV-1 and CoV-2 to design 30 novel noncovalent drug-like pan subgroup 2b PLpro inhibitors that included determining the effects of using previously unexplored core linkers within these compounds. Two crystal structures of BtSCoV-Rf1.2004 PLpro bound to these inhibitors aided in compound design as well as shared structural features among subgroup 2b proteases. Screening of these three subgroup 2b PLpros against this novel set of inhibitors along with cytotoxicity studies provide new directions for pan-coronavirus subgroup 2b antiviral development of PLpro inhibitors.

  • Organizational Affiliation

    Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, 120 W. Green Street, Athens, Georgia 30602, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-like proteinase
A, B
319Bat SARS CoV Rf1/2004Mutation(s): 0 
EC: (PDB Primary Data), (PDB Primary Data)
Find proteins for Q0QDZ2 (Bat SARS CoV Rf1/2004)
Explore Q0QDZ2 
Go to UniProtKB:  Q0QDZ2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ0QDZ2
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.16 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.232 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.385α = 90
b = 67.167β = 90
c = 165.309γ = 90
Software Package:
Software NamePurpose
Cootmodel building
HKL-2000data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI151006

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-02
    Type: Initial release
  • Version 1.1: 2022-03-09
    Changes: Database references
  • Version 1.2: 2022-03-23
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Data collection, Refinement description
  • Version 1.4: 2023-11-15
    Changes: Data collection