2Q6F

Crystal structure of infectious bronchitis virus (IBV) main protease in complex with a Michael acceptor inhibitor N3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.216 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structures of two coronavirus main proteases: implications for substrate binding and antiviral drug design.

Xue, X.Yu, H.Yang, H.Xue, F.Wu, Z.Shen, W.Li, J.Zhou, Z.Ding, Y.Zhao, Q.Zhang, X.C.Liao, M.Bartlam, M.Rao, Z.

(2008) J Virol 82: 2515-2527

  • DOI: 10.1128/JVI.02114-07
  • Primary Citation of Related Structures:  
    2Q6G, 2Q6F, 2Q6D

  • PubMed Abstract: 
  • Coronaviruses (CoVs) can infect humans and multiple species of animals, causing a wide spectrum of diseases. The coronavirus main protease (M(pro)), which plays a pivotal role in viral gene expression and replication through the proteolytic processing of replicase polyproteins, is an attractive target for anti-CoV drug design ...

    Coronaviruses (CoVs) can infect humans and multiple species of animals, causing a wide spectrum of diseases. The coronavirus main protease (M(pro)), which plays a pivotal role in viral gene expression and replication through the proteolytic processing of replicase polyproteins, is an attractive target for anti-CoV drug design. In this study, the crystal structures of infectious bronchitis virus (IBV) M(pro) and a severe acute respiratory syndrome CoV (SARS-CoV) M(pro) mutant (H41A), in complex with an N-terminal autocleavage substrate, were individually determined to elucidate the structural flexibility and substrate binding of M(pro). A monomeric form of IBV M(pro) was identified for the first time in CoV M(pro) structures. A comparison of these two structures to other available M(pro) structures provides new insights for the design of substrate-based inhibitors targeting CoV M(pro)s. Furthermore, a Michael acceptor inhibitor (named N3) was cocrystallized with IBV M(pro) and was found to demonstrate in vitro inactivation of IBV M(pro) and potent antiviral activity against IBV in chicken embryos. This provides a feasible animal model for designing wide-spectrum inhibitors against CoV-associated diseases. The structure-based optimization of N3 has yielded two more efficacious lead compounds, N27 and H16, with potent inhibition against SARS-CoV M(pro).


    Organizational Affiliation

    Laboratory of Structural Biology, Life Sciences Building, Tsinghua University, Beijing 100084, China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Infectious bronchitis virus (IBV) main proteaseA, B309Infectious bronchitis virusMutation(s): 0 
Gene Names: M41 3C-like protease gene
EC: 3.4.22
Find proteins for P0C6V5 (Avian infectious bronchitis virus (strain M41))
Explore P0C6V5 
Go to UniProtKB:  P0C6V5
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
N-[(5-METHYLISOXAZOL-3-YL)CARBONYL]ALANYL-L-VALYL-N~1~-((1R,2Z)-4-(BENZYLOXY)-4-OXO-1-{[(3R)-2-OXOPYRROLIDIN-3-YL]METHYL}BUT-2-ENYL)-L-LEUCINAMIDED [auth C], C [auth D]6synthetic constructMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3IHKi :  3600   nM  PDBBind
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.216 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.175α = 111.06
b = 54.502β = 104.31
c = 66.719γ = 91.33
Software Package:
Software NamePurpose
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-02-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2015-12-02
    Changes: Structure summary