5GWZ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.444 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.1 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

  • PubMed Abstract: 
  • Porcine epidemic diarrhea virus (PEDV) causes high mortality in pigs. PEDV main protease (M <sup>pro </sup>) plays an essential role in viral replication. We solved the structure of PEDV M <sup>pro </sup> complexed with peptidomimetic inhibitor N3 ca ...

    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

    Cleveland Clinic Lerner College of Medicine, Case Western Reserve University , Cleveland, Ohio 44195, United States.,School of Life Sciences, Tianjin University , Tianjin 300072, China.,Department of Molecular Biophysics and Biochemistry, Yale University , New Haven, Connecticut 06520, United States.,Tianjin International Joint Academy of Biotechnology and Medicine , Tianjin 300457, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PEDV main protease
B, A
307Porcine epidemic diarrhea virus (strain CV777)Mutation(s): 0 
Find proteins for P0C6V6 (Porcine epidemic diarrhea virus (strain CV777))
Go to UniProtKB:  P0C6V6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
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-LEUCINAMIDE
D, E
6N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.444 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.185 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 175.263α = 90.00
b = 175.263β = 90.00
c = 58.678γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-03-29
    Type: Initial release
  • Version 1.1: 2017-04-26
    Type: Database references