5GWZ

The structure of Porcine epidemic diarrhea virus main protease in complex with an inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 

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This is version 1.2 of the entry. See complete history


Literature

Michael Acceptor-Based Peptidomimetic Inhibitor of Main Protease from Porcine Epidemic Diarrhea Virus

Wang, F.Chen, C.Yang, K.Xu, Y.Liu, X.Gao, F.Liu, H.Chen, X.Zhao, Q.Liu, X.Cai, Y.Yang, H.

(2017) J Med Chem 60: 3212-3216

  • DOI: 10.1021/acs.jmedchem.7b00103
  • Primary Citation of Related Structures:  
    5GWZ

  • PubMed Abstract: 
  • Porcine epidemic diarrhea virus (PEDV) causes high mortality in pigs. PEDV main protease (M pro ) plays an essential role in viral replication. We solved the structure of PEDV M pro complexed with peptidomimetic inhibitor N3 carrying a Michael acceptor warhead, revealing atomic level interactions ...

    Porcine epidemic diarrhea virus (PEDV) causes high mortality in pigs. PEDV main protease (M pro ) plays an essential role in viral replication. We solved the structure of PEDV M pro complexed with peptidomimetic inhibitor N3 carrying a Michael acceptor warhead, revealing atomic level interactions. We further designed a series of 17 inhibitors with altered side groups. Inhibitors M2 and M17 demonstrated enhanced specificity against PEDV M pro . These compounds have potential as future therapeutics to combat PEDV infection.


    Organizational Affiliation

    Tianjin International Joint Academy of Biotechnology and Medicine , Tianjin 300457, China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PEDV main proteaseB [auth A], A [auth B]307Porcine epidemic diarrhea virus CV777Mutation(s): 0 
Gene Names: 1a
EC: 3.4.22 (PDB Primary Data), 3.4.19.12 (UniProt)
Find proteins for P0C6V6 (Porcine epidemic diarrhea virus (strain CV777))
Explore P0C6V6 
Go to UniProtKB:  P0C6V6
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-LEUCINAMIDEC [auth D], D [auth E]6synthetic constructMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 175.263α = 90
b = 175.263β = 90
c = 58.678γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-29
    Type: Initial release
  • Version 1.1: 2017-04-26
    Changes: Database references
  • Version 1.2: 2020-02-26
    Changes: Data collection