5E0H

1.95 A resolution structure of Norovirus 3CL protease in complex with a triazole-based macrocyclic (18-mer) inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


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

  • 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.


  • Organizational Affiliation

    Department of Chemistry, Wichita State University, Wichita, KS 67260, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Norovirus 3C-like protease
A, B
188Norovirus Hu/1968/USMutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ83883
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
5LH
Query on 5LH

Download Ideal Coordinates CCD File 
C [auth A](phenylmethyl) ~{N}-[(9~{S},12~{S},15~{S})-9-(hydroxymethyl)-12-(2-methylpropyl)-6,11,14-tris(oxidanylidene)-1,5,10,13,18,19-hexazabicyclo[15.2.1]icosa-17(20),18-dien-15-yl]carbamate
C27 H39 N7 O6
SAMHMGNFOZHCAI-PMVMPFDFSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.102α = 94
b = 48.772β = 109.5
c = 53.083γ = 101.29
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States5R01AI109039

Revision History  (Full details and data files)

  • 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