Structure of the SARS-CoV-2 3CL protease in complex with rupintrivir

Experimental Data Snapshot

  • Resolution: 2.26 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.200 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.1 of the entry. See complete history


Structure and inhibition of SARS-CoV-1 and SARS-CoV-2 main proteases by oral antiviral compound AG7404.

Fabrega-Ferrer, M.Herrera-Morande, A.Muriel-Goni, S.Perez-Saavedra, J.Bueno, P.Castro, V.Garaigorta, U.Gastaminza, P.Coll, M.

(2022) Antiviral Res 208: 105458-105458

  • DOI: https://doi.org/10.1016/j.antiviral.2022.105458
  • Primary Citation of Related Structures:  
    7P35, 7ZQV, 7ZQW

  • PubMed Abstract: 

    Severe acute respiratory syndrome coronaviruses 1 and 2 (SARS-CoV-1 and SARS-CoV-2) pose a threat to global public health. The 3C-like main protease (M pro ), which presents structural similarity with the active site domain of enterovirus 3C protease, is one of the best-characterized drug targets of these viruses. Here we studied the antiviral activity of the orally bioavailable enterovirus protease inhibitor AG7404 against SARS-CoV-1 and SARS-CoV-2 from a structural, biochemical, and cellular perspective, comparing it with the related molecule rupintrivir (AG7800). Crystallographic structures of AG7404 in complex with SARS-CoV-1 M pro and SARS-CoV-2 M pro and of rupintrivir in complex with SARS-CoV-2 M pro were solved, revealing that all protein residues interacting with the inhibitors are conserved between the two proteins. A detailed analysis of protein-inhibitor interactions indicates that AG7404 has a better fit to the active site of the target protease than rupintrivir. This observation was further confirmed by biochemical FRET assays showing IC 50 values of 47 μM and 101 μM for AG7404 and rupintrivir, respectively, in the case of SARS-CoV-2 M pro . Equivalent IC 50 values for SARS-CoV-1 also revealed greater inhibitory capacity of AG7404, with a value of 29 μM vs. 66 μM for rupintrivir. Finally, the antiviral activity of the two inhibitors against SARS-CoV-2 was confirmed in a human cell culture model of SARS-CoV-2 infection, although rupintrivir showed a higher potency and selectivity index in this assay.

  • Organizational Affiliation

    Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028, Barcelona, Spain; Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Baldiri Reixac 10, Barcelona, 08028, Spain.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-like proteinaseA [auth AAA],
B [auth BBB]
306Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: ORF1ab
EC: (PDB Primary Data), (PDB Primary Data), (PDB Primary Data), (PDB Primary Data), (PDB Primary Data)
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AG7 (Subject of Investigation/LOI)
Query on AG7

Download Ideal Coordinates CCD File 
C [auth AAA],
D [auth BBB]
C31 H41 F N4 O7
Experimental Data & Validation

Experimental Data

  • Resolution: 2.26 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.200 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.023α = 90
b = 54.024β = 100.774
c = 114.067γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Spanish Ministry of Science, Innovation, and UniversitiesSpainBFU2017-83720-P
Spanish National Research CouncilSpainAEPP2020

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-21
    Type: Initial release
  • Version 1.1: 2022-12-28
    Changes: Database references, Derived calculations