7QKA

Crystal structure of SARS-CoV-2 Main Protease in complex with covalently bound GC376


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.167 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Calpeptin is a potent cathepsin inhibitor and drug candidate for SARS-CoV-2 infections.

Reinke, P.Y.A.de Souza, E.E.Gunther, S.Falke, S.Lieske, J.Ewert, W.Loboda, J.Herrmann, A.Rahmani Mashhour, A.Karnicar, K.Usenik, A.Lindic, N.Sekirnik, A.Botosso, V.F.Santelli, G.M.M.Kapronezai, J.de Araujo, M.V.Silva-Pereira, T.T.Filho, A.F.S.Tavares, M.S.Florez-Alvarez, L.de Oliveira, D.B.L.Durigon, E.L.Giaretta, P.R.Heinemann, M.B.Hauser, M.Seychell, B.Bohler, H.Rut, W.Drag, M.Beck, T.Cox, R.Chapman, H.N.Betzel, C.Brehm, W.Hinrichs, W.Ebert, G.Latham, S.L.Guimaraes, A.M.S.Turk, D.Wrenger, C.Meents, A.

(2023) Commun Biol 6: 1058-1058

  • DOI: https://doi.org/10.1038/s42003-023-05317-9
  • Primary Citation of Related Structures:  
    7QGW, 7QKA, 7QKB, 7QKC, 7Z3T, 7Z3U, 7Z58, 8C3D

  • PubMed Abstract: 

    Several drug screening campaigns identified Calpeptin as a drug candidate against SARS-CoV-2. Initially reported to target the viral main protease (M pro ), its moderate activity in M pro inhibition assays hints at a second target. Indeed, we show that Calpeptin is an extremely potent cysteine cathepsin inhibitor, a finding additionally supported by X-ray crystallography. Cell infection assays proved Calpeptin's efficacy against SARS-CoV-2. Treatment of SARS-CoV-2-infected Golden Syrian hamsters with sulfonated Calpeptin at a dose of 1 mg/kg body weight reduces the viral load in the trachea. Despite a higher risk of side effects, an intrinsic advantage in targeting host proteins is their mutational stability in contrast to highly mutable viral targets. Here we show that the inhibition of cathepsins, a protein family of the host organism, by calpeptin is a promising approach for the treatment of SARS-CoV-2 and potentially other viral infections.


  • Organizational Affiliation

    Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-like proteinase nsp5306Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.167 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.675α = 90
b = 53.356β = 102.511
c = 44.994γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Helmholtz AssociationGermanyFISCOV
Helmholtz AssociationGermanySFragX
German Federal Ministry for Education and ResearchGermany16GW0277
Slovenian Research AgencySloveniaP1-0048
Slovenian Research AgencySloveniaIO-0048

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-28
    Type: Initial release
  • Version 1.1: 2023-11-01
    Changes: Author supporting evidence, Data collection, Database references
  • Version 1.2: 2024-01-31
    Changes: Refinement description