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 
  • R-Value Observed: 0.190 

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Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1016/j.ejmech.2017.12.014
  • Primary Citation of Related Structures:  
    5WEJ

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Genome polyprotein
A, B
188Norovirus Hu/1968/USMutation(s): 0 
Gene Names: ORF1
EC: 3.6.1.15 (PDB Primary Data), 3.4.22.66 (PDB Primary Data), 2.7.7.48 (PDB Primary Data)
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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
V45
Query on V45

Download Ideal Coordinates CCD File 
C [auth A],
D [auth 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.556α = 90
b = 59.556β = 90
c = 357.548γ = 120
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



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 StatesAI109039
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP30GM110761

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-13
    Type: Initial release
  • Version 1.1: 2017-12-27
    Changes: Database references
  • Version 1.2: 2019-12-11
    Changes: Author supporting evidence
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Refinement description