2GX4

Crystal structure of SARS coronavirus 3CL protease inhibitor complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

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: 10.1021/jm0603926
  • Primary Citation of Related Structures:  
    2GX4

  • 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 mic ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3C-like proteinaseA306Severe acute respiratory syndrome-related coronavirusMutation(s): 0 
Gene Names: rep1a-1b
EC: 3.4.22 (PDB Primary Data), 3.4.19.12 (UniProt), 3.4.22.69 (UniProt), 2.7.7.48 (UniProt), 3.6.4.12 (UniProt), 3.6.4.13 (UniProt), 2.1.1 (UniProt), 3.1.13 (UniProt), 3.1 (UniProt)
Find proteins for P0C6X7 (Severe acute respiratory syndrome coronavirus)
Explore P0C6X7 
Go to UniProtKB:  P0C6X7
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NOL
Query on NOL

Download CCD File 
A
N-[(BENZYLOXY)CARBONYL]-O-(TERT-BUTYL)-L-THREONYL-3-CYCLOHEXYL-N-[(1S)-2-HYDROXY-1-{[(3S)-2-OXOPYRROLIDIN-3-YL]METHYL}ETHYL]-L-ALANINAMIDE
C32 H50 N4 O7
YIWYOEOSWRXENJ-FFXRMZKPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
AMoREphasing
CNSrefinement
CrystalCleardata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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