2.26 A resolution structure of MERS 3CL protease in complex with inhibitor 7i

Experimental Data Snapshot

  • Resolution: 2.26 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.187 

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This is version 1.3 of the entry. See complete history


3C-like protease inhibitors block coronavirus replication in vitro and improve survival in MERS-CoV-infected mice.

Rathnayake, A.D.Zheng, J.Kim, Y.Perera, K.D.Mackin, S.Meyerholz, D.K.Kashipathy, M.M.Battaile, K.P.Lovell, S.Perlman, S.Groutas, W.C.Chang, K.O.

(2020) Sci Transl Med 12

  • DOI: https://doi.org/10.1126/scitranslmed.abc5332
  • Primary Citation of Related Structures:  
    6VGY, 6VGZ, 6VH0, 6VH1, 6VH2, 6VH3, 6W2A, 6XMK

  • PubMed Abstract: 

    Pathogenic coronaviruses are a major threat to global public health, as exemplified by severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), and the newly emerged SARS-CoV-2, the causative agent of coronavirus disease 2019 (COVID-19). We describe herein the structure-guided optimization of a series of inhibitors of the coronavirus 3C-like protease (3CLpro), an enzyme essential for viral replication. The optimized compounds were effective against several human coronaviruses including MERS-CoV, SARS-CoV, and SARS-CoV-2 in an enzyme assay and in cell-based assays using Huh-7 and Vero E6 cell lines. Two selected compounds showed antiviral effects against SARS-CoV-2 in cultured primary human airway epithelial cells. In a mouse model of MERS-CoV infection, administration of a lead compound 1 day after virus infection increased survival from 0 to 100% and reduced lung viral titers and lung histopathology. These results suggest that this series of compounds has the potential to be developed further as antiviral drugs against human coronaviruses.

  • Organizational Affiliation

    Department of Chemistry, Wichita State University, Wichita, KS 67260, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Orf1a protein
A, B
313Middle East respiratory syndrome-related coronavirusMutation(s): 0 
Gene Names: orf1a
Find proteins for T2B9U0 (Middle East respiratory syndrome-related coronavirus)
Explore T2B9U0 
Go to UniProtKB:  T2B9U0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupT2B9U0
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QZ4 (Subject of Investigation/LOI)
Query on QZ4

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
4,4-difluorocyclohexyl [(2S)-3-cyclohexyl-1-({(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}amino)-1-oxopropan-2-yl]carbamate
C23 H37 F2 N3 O5
Experimental Data & Validation

Experimental Data

  • Resolution: 2.26 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.187 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.028α = 90
b = 91.098β = 90
c = 100.777γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP30GM110761
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI109039

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-12
    Type: Initial release
  • Version 1.1: 2020-08-19
    Changes: Database references
  • Version 1.2: 2020-09-02
    Changes: Database references
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Refinement description