5WEJ

1.95 A resolution structure of Norovirus 3CL protease in complex with a dipeptidyl oxazolidinone-based inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure-guided design, synthesis and evaluation of oxazolidinone-based inhibitors of norovirus 3CL protease.

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

(2017) Eur J Med Chem 143: 881-890

  • DOI: 10.1016/j.ejmech.2017.12.014

  • PubMed Abstract: 
  • Acute nonbacterial gastroenteritis caused by noroviruses constitutes a global public health concern and a significant economic burden. There are currently no small molecule therapeutics or vaccines for the treatment of norovirus infections. A structu ...

    Acute nonbacterial gastroenteritis caused by noroviruses constitutes a global public health concern and a significant economic burden. There are currently no small molecule therapeutics or vaccines for the treatment of norovirus infections. A structure-guided approach was utilized in the design of a series of inhibitors of norovirus 3CL protease that embody an oxazolidinone ring as a novel design element for attaining optimal binding interactions. Low micromolar cell-permeable inhibitors that display anti-norovirus activity have been identified. The mechanism of action, mode of binding, and structural rearrangements associated with the interaction of the inhibitors and the enzyme were elucidated using X-ray crystallography.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Genome polyprotein
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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
V45
Query on V45

Download SDF File 
Download CCD File 
A, B
(2S)-2-{(5S)-5-[(3-chlorophenyl)methyl]-2-oxo-1,3-oxazolidin-3-yl}-4-methyl-N-{(2S)-1-oxo-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}pentanamide
C23 H30 Cl N3 O5
HPMLVVHQNDVVJA-ZXBFEJPJSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.188 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 59.556α = 90.00
b = 59.556β = 90.00
c = 357.548γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
Aimlessdata scaling
PHENIXrefinement
XDSdata reduction
PDB_EXTRACTdata extraction

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: 2017-12-13
    Type: Initial release
  • Version 1.1: 2017-12-27
    Type: Database references