5TG2 | pdb_00005tg2

1.75 A resolution structure of Norovirus 3CL protease in complex with the a n-pentyl substituted macrocyclic inhibitor (17-mer)

• PDB DOI: https://doi.org/10.2210/pdb5TG2/pdb

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


• Deposited: 2016-09-27 Released: 2017-01-11 
• Deposition Author(s): Lovell, S., Battaile, K.P., Mehzabeen, N., Damalanka, V.C., Kim, Y., Kankanamalage, A.C.G., Chang, K.-O., Groutas, W.C.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.227 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Starting Model: experimental

Literature

Design, synthesis, and evaluation of a novel series of macrocyclic inhibitors of norovirus 3CL protease.

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

(2016) Eur J Med Chem 127: 41-61

• PubMed: 28038326 
• DOI: https://doi.org/10.1016/j.ejmech.2016.12.033
• Primary Citation Related Structures: 
  5TG1, 5TG2


• PubMed Abstract: 
  

  Norovirus infections have a major impact on public health worldwide, yet there is a current dearth of norovirus-specific therapeutics and prophylactics. This report describes the discovery of a novel class of macrocyclic inhibitors of norovirus 3C-like protease, a cysteine protease that is essential for virus replication. SAR, structural, and biochemical studies were carried out to ascertain the effect of structure on pharmacological activity and permeability. Insights gained from these studies have laid a solid foundation for capitalizing on the therapeutic potential of the series of inhibitors described herein.

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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.

Macromolecule Content 

• Total Structure Weight: 20.57 kDa 
• Atom Count: 1,310 
• Modeled Residue Count: 162 
• 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
V69	B [auth A]	(4S,7S,17R)-7-(hydroxymethyl)-4-(2-methylpropyl)-17-pentyl-1-oxa-3,6,11-triazacycloheptadecane-2,5,10-trione C23 H43 N3 O5 RKQBXGIWUUASPA-ZCNNSNEGSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002248 (V69)	B [auth A]	(4S,7S,17R)-7-(hydroxymethyl)-4-(2-methylpropyl)-17-pentyl-1-oxa-3,6,11-triazacycloheptadecane-2,5,10-trione	Cyclic peptide / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.227 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.02	α = 90
b = 36.703	β = 110.23
c = 61.721	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: 2017-01-11 
Deposition Author(s): Lovell, S., Battaile, K.P., Mehzabeen, N., Damalanka, V.C., Kim, Y., Kankanamalage, A.C.G., 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	AI109039
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P30GM110761

Revision History  

• Version 1.0: 2017-01-11
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Author supporting evidence
• Version 1.2: 2019-12-11
  Changes: Author supporting evidence
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-11-20
  Changes: Structure summary