5TG2

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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

  • DOI: 10.1016/j.ejmech.2016.12.033
  • Primary Citation of Related Structures:  

  • 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-li ...

    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.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
3C-LIKE PROTEASE
A
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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
V69
Query on V69

Download SDF File 
Download CCD File 
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
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_002248 (V69)
Query on PRD_002248
ACyclic peptide / Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.176 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 67.020α = 90.00
b = 36.703β = 110.23
c = 61.721γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PDB_EXTRACTdata extraction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement

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 StatesAI109039
National Institutes of Health/National Institute of General Medical SciencesUnited StatesP30GM110761

Revision History 

  • Version 1.0: 2017-01-11
    Type: Initial release
  • Version 1.1: 2017-09-27
    Type: Author supporting evidence