6W81 | pdb_00006w81

Structure of PEDV main protease bound to potent broad-spectrum non-covalent inhibitor X77

• PDB DOI: https://doi.org/10.2210/pdb6W81/pdb

• Classification: VIRAL PROTEIN/INHIBITOR
• Organism(s): Porcine epidemic diarrhea virus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-03-20 Released: 2021-03-24 
• Deposition Author(s): Mesecar, A.D., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.214 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

A taxonomically-driven approach to development of potent, broad-spectrum inhibitors of coronavirus main protease including SARS-CoV-2 (COVID-19)

Mesecar, A.D.

To be published.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 66.66 kDa 
• Atom Count: 5,251 
• Modeled Residue Count: 602 
• Deposited Residue Count: 604 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidase C30	A, B	302	Porcine epidemic diarrhea virus	Mutation(s): 0  Gene Names: ORF1ab
UniProt
Find proteins for A0A059VJE6 (Porcine epidemic diarrhea virus) Explore A0A059VJE6  Go to UniProtKB:  A0A059VJE6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
X77 (Subject of Investigation/LOI)	C [auth A], D [auth B]	N-(4-tert-butylphenyl)-N-[(1R)-2-(cyclohexylamino)-2-oxo-1-(pyridin-3-yl)ethyl]-1H-imidazole-4-carboxamide C27 H33 N5 O2 MUNFBYOTGGMQOS-XMMPIXPASA-N
MLA	E [auth B]	MALONIC ACID C3 H4 O4 OFOBLEOULBTSOW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.214 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.679	α = 90
b = 85.257	β = 100.46
c = 58.186	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-03-24 
Deposition Author(s): Mesecar, A.D., Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700060C

Revision History  

• Version 1.0: 2021-03-24
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description