Crystal structures of the SARS-coronavirus main proteinase inactivated by benzotriazole compounds

Experimental Data Snapshot

  • Resolution: 1.98 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


A Structural View of the Inactivation of the Sars Coronavirus Main Proteinase by Benzotriazole Esters.

Verschueren, K.H.G.Pumpor, K.Anemueller, S.Chen, S.Mesters, J.R.Hilgenfeld, R.

(2008) Chem Biol 15: 597

  • DOI: https://doi.org/10.1016/j.chembiol.2008.04.011
  • Primary Citation of Related Structures:  
    2V6N, 2VJ1

  • PubMed Abstract: 

    The main proteinase (M(pro)) of the severe acute respiratory syndrome (SARS) coronavirus is a principal target for the design of anticoronaviral compounds. Benzotriazole esters have been reported as potent nonpeptidic inhibitors of the enzyme, but their exact mechanism of action remains unclear. Here we present crystal structures of SARS-CoV M(pro), the active-site cysteine of which has been acylated by benzotriazole esters that act as suicide inhibitors. In one of the structures, the thioester product has been hydrolyzed and benzoic acid is observed to bind to the hydrophobic S2 pocket. This structure also features the enzyme with a shortened N-terminal segment ("amputated N finger"). The results further the understanding of the important role of the N finger for catalysis as well as the design of benzotriazole inhibitors with improved specificity.

  • Organizational Affiliation

    Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Lübeck, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
REPLICASE POLYPROTEIN 1AB306Severe acute respiratory syndrome-related coronavirusMutation(s): 0 
EC: 3.4.24
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
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
XP1 PDBBind:  2V6N Ki: 1380 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.98 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.265α = 90
b = 81.974β = 104.3
c = 53.418γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-07-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2019-07-24
    Changes: Data collection, Derived calculations
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Other, Refinement description