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 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1016/j.ejmech.2016.04.013
  • Primary Citation of Related Structures:  

  • 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 t ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Norovirus 3C-like protease
A, B
188Norwalk virus (strain GI/Human/United States/Norwalk/1968)Mutation(s): 0 
Find proteins for Q83883 (Norwalk virus (strain GI/Human/United States/Norwalk/1968))
Go to UniProtKB:  Q83883
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
5LH
Query on 5LH

Download SDF File 
Download CCD File 
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
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.183 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 38.102α = 94.00
b = 48.772β = 109.50
c = 53.083γ = 101.29
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited States5R01AI109039

Revision History 

  • Version 1.0: 2016-05-04
    Type: Initial release
  • Version 1.1: 2016-06-15
    Type: Database references
  • Version 1.2: 2017-09-13
    Type: Author supporting evidence, Database references, Derived calculations