5E0J | pdb_00005e0j

1.20 A resolution structure of Norovirus 3CL protease in complex with a triazole-based macrocyclic (21-mer) inhibitor

• PDB DOI: https://doi.org/10.2210/pdb5E0J/pdb

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


• Deposited: 2015-09-28 Released: 2016-05-04 
• Deposition Author(s): Lovell, S., Battaile, K.P., Mehzabeen, N., Weerawarna, P.M., Kim, Y., Kankanamalage, A.C.G., Damalanka, V.C., Lushington, G.H., Alliston, K.R., 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: 1.20 Å
• R-Value Free: 
  0.165 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.137 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.138 (Depositor) 

Starting Model: experimental

Literature

Structure-based design and synthesis of triazole-based macrocyclic inhibitors of norovirus protease: Structural, biochemical, spectroscopic, and antiviral studies.

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

(2016) Eur J Med Chem 119: 300-318

• PubMed: 27235842 
• DOI: https://doi.org/10.1016/j.ejmech.2016.04.013
• Primary Citation of Related Structures:  
  5E0G, 5E0H, 5E0J


• PubMed Abstract: 
  

  Outbreaks of acute gastroenteritis caused by noroviruses constitute a public health concern worldwide. To date, there are no approved drugs or vaccines for the management and prophylaxis of norovirus infections. A potentially effective strategy for the development of norovirus therapeutics entails the discovery of inhibitors of norovirus 3CL protease, an enzyme essential for noroviral replication. We describe herein the structure-based design of the first class of permeable, triazole-based macrocyclic inhibitors of norovirus 3C-like protease, as well as pertinent X-ray crystallographic, biochemical, spectroscopic, and antiviral studies.

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Organizational Affiliation: 
• Department of Chemistry, Wichita State University, Wichita, KS 67260, USA.
Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA.
LiS Consulting, Lawrence, KS 66046, USA.
Protein Structure Laboratory, The University of Kansas, Lawrence, KS 66047, USA.
IMCA-CAT, Hauptman-Woodward Medical Research Institute, APS Argonne National Laboratory, Argonne, IL 60439, USA.
Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA. Electronic address: [e-mail].
Department of Chemistry, Wichita State University, Wichita, KS 67260, USA. Electronic address: [e-mail].

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: 20.87 kDa 
• Atom Count: 1,514 
• Modeled Residue Count: 174 
• Deposited Residue Count: 188 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Norovirus 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5LJ	E [auth A]	(phenylmethyl) ~{N}-[(12~{S},15~{S},18~{S})-15-(cyclohexylmethyl)-12-(hydroxymethyl)-9,14,17-tris(oxidanylidene)-1,8,13,16,21,22-hexazabicyclo[18.2.1]tricosa-20(23),21-dien-18-yl]carbamate C33 H49 N7 O6 ITOVOSDUKDWVAY-ZXRKZBAXSA-N
CL	B [auth A], C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002203 (5LJ)	E [auth A]	(phenylmethyl) ~{N}-[(12~{S},15~{S},18~{S})-15-(cyclohexylmethyl)-12-(hydroxymethyl)-9,14,17-tris(oxidanylidene)-1,8,13,16,21,22-hexazabicyclo[18.2.1]tricosa-20(23),21-dien-18-yl]carbamate	Polypeptide / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free:  0.165 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.137 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.138 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.666	α = 90
b = 37.159	β = 110.04
c = 61.859	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-05-04 
Deposition Author(s): Lovell, S., Battaile, K.P., Mehzabeen, N., Weerawarna, P.M., Kim, Y., Kankanamalage, A.C.G., Damalanka, V.C., Lushington, G.H., Alliston, K.R., 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	5R01AI109039

Revision History  

• Version 1.0: 2016-05-04
  Type: Initial release
  
• Version 1.1: 2016-06-15
  Changes: Database references
• Version 1.2: 2017-09-13
  Changes: Author supporting evidence, Database references, Derived calculations
• Version 1.3: 2019-12-11
  Changes: Author supporting evidence
• Version 1.4: 2023-09-27
  Changes: Data collection, Database references, Refinement description
• Version 1.5: 2024-11-06
  Changes: Structure summary