2GZ9

Structure-Based Drug Design and Structural Biology Study of Novel Nonpeptide Inhibitors of SARS-CoV Main Protease


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure-Based Drug Design and Structural Biology Study of Novel Nonpeptide Inhibitors of Severe Acute Respiratory Syndrome Coronavirus Main Protease

Lu, I.L.Mahindroo, N.Liang, P.H.Peng, Y.H.Kuo, C.J.Tsai, K.C.Hsieh, H.P.Chao, Y.S.Wu, S.Y.

(2006) J Med Chem 49: 5154-5161

  • DOI: 10.1021/jm060207o
  • Primary Citation of Related Structures:  
    2GZ9, 2GZ8, 2GZ7

  • PubMed Abstract: 
  • Severe acute respiratory syndrome coronavirus (SARS-CoV) main protease (M(pro)), a protein required for the maturation of SARS-CoV, is vital for its life cycle, making it an attractive target for structure-based drug design of anti-SARS drugs. The st ...

    Severe acute respiratory syndrome coronavirus (SARS-CoV) main protease (M(pro)), a protein required for the maturation of SARS-CoV, is vital for its life cycle, making it an attractive target for structure-based drug design of anti-SARS drugs. The structure-based virtual screening of a chemical database containing 58,855 compounds followed by the testing of potential compounds for SARS-CoV M(pro) inhibition leads to two hit compounds. The core structures of these two hits, defined by the docking study, are used for further analogue search. Twenty-one analogues derived from these two hits exhibited IC50 values below 50 microM, with the most potent one showing 0.3 microM. Furthermore, the complex structures of two potent inhibitors with SARS-CoV M(pro) were solved by X-ray crystallography. They bind to the protein in a distinct manner compared to all published SARS-CoV M(pro) complex structures. They inhibit SARS-CoV M(pro) activity via intensive H-bond network and hydrophobic interactions, without the formation of a covalent bond. Interestingly, the most potent inhibitor induces protein conformational changes, and the inhibition mechanisms, particularly the disruption of catalytic dyad (His41 and Cys145), are elaborated.


    Organizational Affiliation

    Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan, Republic of China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Replicase polyprotein 1abA306Severe 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 (Human SARS coronavirus)
Explore P0C6X7 
Go to UniProtKB:  P0C6X7
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.217 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.195α = 90
b = 82.419β = 104.98
c = 53.609γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2006-05-11 
  • Released Date: 2006-08-29 
  • Deposition Author(s): Lu, I.L., Wu, S.Y.

Revision History 

  • Version 1.0: 2006-08-29
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance