Crystal structure of SARS coronavirus 3CL protease inhibitor complex

Experimental Data Snapshot

  • Resolution: 1.93 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.205 

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This is version 1.3 of the entry. See complete history


Synthesis, crystal structure, structure-activity relationships, and antiviral activity of a potent SARS coronavirus 3CL protease inhibitor.

Yang, S.Chen, S.J.Hsu, M.F.Wu, J.D.Tseng, C.T.Liu, Y.F.Chen, H.C.Kuo, C.W.Wu, C.S.Chang, L.W.Chen, W.C.Liao, S.Y.Chang, T.Y.Hung, H.H.Shr, H.L.Liu, C.Y.Huang, Y.A.Chang, L.Y.Hsu, J.C.Peters, C.J.Wang, A.H.Hsu, M.C.

(2006) J Med Chem 49: 4971-4980

  • DOI: https://doi.org/10.1021/jm0603926
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    A potent SARS coronavirus (CoV) 3CL protease inhibitor (TG-0205221, Ki = 53 nM) has been developed. TG-0205221 showed remarkable activity against SARS CoV and human coronavirus (HCoV) 229E replications by reducing the viral titer by 4.7 log (at 5 microM) for SARS CoV and 5.2 log (at 1.25 microM) for HCoV 229E. The crystal structure of TG-0205221 (resolution = 1.93 A) has revealed a unique binding mode comprising a covalent bond, hydrogen bonds, and numerous hydrophobic interactions. Structural comparisons between TG-0205221 and a natural peptide substrate were also discussed. This information may be applied toward the design of other 3CL protease inhibitors.

  • Organizational Affiliation

    TaiGen Biotechnology Co., Taipei 114, Taiwan, ROC.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-like proteinase306Severe acute respiratory syndrome-related coronavirusMutation(s): 0 
EC: 3.4.22
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
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NOL

Download Ideal Coordinates CCD File 
C32 H50 N4 O7
Experimental Data & Validation

Experimental Data

  • Resolution: 1.93 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.205 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.029α = 90
b = 81.16β = 104.73
c = 53.289γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
DENZOdata reduction
CrystalCleardata 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: 2007-05-08
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2020-04-08
    Changes: Database references, Derived calculations