5DGJ

1.0A resolution structure of Norovirus 3CL protease in complex an oxadiazole-based, cell permeable macrocyclic (20-mer) inhibitor

• PDB DOI: https://doi.org/10.2210/pdb5DGJ/pdb

• Classification: HYDROLASE/HYDROLASE inhibitor
• Organism(s): Norovirus Hu/1968/US
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2015-08-27 Released: 2016-02-10 
• Deposition Author(s): Lovell, S., Battaile, K.P., Mehzabeen, N., Damalanka, V.C., Kim, Y., Alliston, K.R., Weerawarna, P.M., Kankanamalage, A.C.G., Lushington, G.H., Chang, K.-O., Groutas, W.C.
• 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: 1.00 Å
• R-Value Free: 0.154 
• R-Value Work: 0.143 
• R-Value Observed: 0.143 

Starting Model: experimental

Literature

Oxadiazole-Based Cell Permeable Macrocyclic Transition State Inhibitors of Norovirus 3CL Protease.

Damalanka, V.C., Kim, Y., Alliston, K.R., Weerawarna, P.M., Galasiti Kankanamalage, A.C., Lushington, G.H., Mehzabeen, N., Battaile, K.P., Lovell, S., Chang, K.O., Groutas, W.C.

(2016) J Med Chem 59: 1899-1913

• PubMed: 26823007 
• DOI: https://doi.org/10.1021/acs.jmedchem.5b01464
• Primary Citation of Related Structures:  
  5DG6, 5DGJ


• PubMed Abstract: 
  

  Human noroviruses are the primary causative agents of acute gastroenteritis and a pressing public health burden worldwide. There are currently no vaccines or small molecule therapeutics available for the treatment or prophylaxis of norovirus infections. Norovirus 3CL protease plays a vital role in viral replication by generating structural and nonstructural proteins via the cleavage of the viral polyprotein. Thus, molecules that inhibit the viral protease may have potential therapeutic value. We describe herein the structure-based design, synthesis, and in vitro and cell-based evaluation of the first class of oxadiazole-based, permeable macrocyclic inhibitors of norovirus 3CL protease.

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Organizational Affiliation: 

Department of Chemistry, Wichita State University , Wichita, Kansas 67260, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 20.72 kDa 
• Atom Count: 1,485 
• Modelled Residue Count: 168 
• Deposited Residue Count: 188 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-LIKE PROTEASE	A	188	Norovirus Hu/1968/US	Mutation(s): 0  Gene Names: ORF1 EC: 3.4.22.66
UniProt
Find proteins for Q83883 (Norovirus (strain Human/NoV/United States/Norwalk/1968/GI)) Explore Q83883  Go to UniProtKB:  Q83883

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
V64	B [auth A]	tert-butyl [(4S,7S,10S)-7-(cyclohexylmethyl)-10-(hydroxymethyl)-5,8,13-trioxo-22-oxa-6,9,14,20,21-pentaazabicyclo[17.2.1]docosa-1(21),19-dien-4-yl]carbamate C29 H48 N6 O7 GGHACTZVDKMERX-FKBYEOEOSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002189 (V64)	B [auth A]	tert-butyl [(4S,7S,10S)-7-(cyclohexylmethyl)-10-(hydroxymethyl)-5,8,13-trioxo-22-oxa-6,9,14,20,21-pentaazabicyclo[17.2.1]docosa-1(21),19-dien-4-yl]carbamate	Peptide-like / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free: 0.154 
• R-Value Work: 0.143 
• R-Value Observed: 0.143 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.169	α = 90
b = 41.176	β = 109.36
c = 61.679	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-02-10 
Deposition Author(s): Lovell, S., Battaile, K.P., Mehzabeen, N., Damalanka, V.C., Kim, Y., Alliston, K.R., Weerawarna, P.M., Kankanamalage, A.C.G., Lushington, G.H., Chang, K.-O., Groutas, W.C.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01 AI109039

Revision History  

• Version 1.0: 2016-02-10
  Type: Initial release
  
• Version 1.1: 2016-02-17
  Changes: Database references
• Version 1.2: 2016-03-23
  Changes: Database references
• Version 1.3: 2017-09-27
  Changes: Author supporting evidence, Database references, Derived calculations
• Version 1.4: 2019-12-11
  Changes: Author supporting evidence
• Version 1.5: 2020-08-12
  Changes: Structure summary
• Version 1.6: 2023-09-27
  Changes: Data collection, Database references, Refinement description
• Version 1.7: 2024-11-20
  Changes: Structure summary