2GZ7

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: 1.856 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.204 

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:  2GZ8, 2GZ9

  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Replicase polyprotein 1ab
A
306SARS coronavirus TW6N/A
Find proteins for Q6RCZ9 (SARS coronavirus TW6)
Go to UniProtKB:  Q6RCZ9
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
D3F
Query on D3F

Download SDF File 
Download CCD File 
A
2-[(2,4-DICHLORO-5-METHYLPHENYL)SULFONYL]-1,3-DINITRO-5-(TRIFLUOROMETHYL)BENZENE
2-[(2,4-DICHLORO-5-METHYLPHENYL)SULFONYL]-1,3-DINITRO-5-(TRIFLUOROMETHYL) BENZENE
C14 H7 Cl2 F3 N2 O6 S
INAZPZCJNPPHGV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
D3FIC50: 300 nM (100) BINDINGDB
D3FIC50: 300 nM BINDINGMOAD
D3FIC50: 300 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.856 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.204 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 107.776α = 90.00
b = 82.777β = 104.93
c = 53.579γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data collection
REFMACrefinement
MOLREPphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance