5GWZ | pdb_00005gwz

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

• PDB DOI: https://doi.org/10.2210/pdb5GWZ/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Porcine epidemic diarrhea virus CV777, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-09-14 Released: 2017-03-29 
• Deposition Author(s): Wang, F., Chen, C., Yang, K., Liu, X., Liu, H., Xu, Y., Chen, X., Liu, X., Cai, Y., Yang, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.44 Å
• R-Value Free: 
  0.219 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: experimental

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

• PubMed: 28287727 
• DOI: https://doi.org/10.1021/acs.jmedchem.7b00103
• Primary Citation 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. 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.

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 67.69 kDa 
• Atom Count: 4,857 
• Modeled Residue Count: 610 
• Deposited Residue Count: 626 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PEDV main protease	A [auth B], B [auth A]	307	Porcine epidemic diarrhea virus CV777	Mutation(s): 0  Gene Names: 1a EC: 3.4.22
UniProt
Find proteins for P0C6V6 (Porcine epidemic diarrhea virus (strain CV777)) Explore P0C6V6  Go to UniProtKB:  P0C6V6

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
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	C [auth D], D [auth E]	6	synthetic construct	Mutation(s): 0

Small Molecules

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
02J	C [auth D], D [auth E]	PEPTIDE-LIKE	C5 H5 N O3		--
PJE	C [auth D], D [auth E]	PEPTIDE-LIKE	C9 H14 N2 O3		--

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002214	C [auth D], D [auth E]	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	Peptide-like / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.44 Å
• R-Value Free:  0.219 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 175.263	α = 90
b = 175.263	β = 90
c = 58.678	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-03-29 
Deposition Author(s): Wang, F., Chen, C., Yang, K., Liu, X., Liu, H., Xu, Y., Chen, X., Liu, X., Cai, Y., Yang, H.

Revision History  

• 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
• Version 1.3: 2023-11-08
  Changes: Data collection, Database references, Refinement description
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Derived calculations
• Version 2.1: 2024-10-23
  Changes: Structure summary