5DGJ

1.0A resolution structure of Norovirus 3CL protease in complex an oxadiazole-based, cell permeable macrocyclic (20-mer) inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.00 Å
  • R-Value Free: 0.154 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.143 

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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

Oxadiazole-Based Cell Permeable Macrocyclic Transition State Inhibitors of Norovirus 3CL Protease.

Damalanka, V.C.Kim, Y.Alliston, K.R.Weerawarna, P.M.Galasiti Kankanamalage, A.C.Lushington, G.H.Mehzabeen, N.Battaile, K.P.Lovell, S.Chang, K.O.Groutas, W.C.

(2016) J Med Chem 59: 1899-1913

  • DOI: 10.1021/acs.jmedchem.5b01464
  • Primary Citation of Related Structures:  
    5DG6, 5DGJ

  • PubMed Abstract: 
  • Human noroviruses are the primary causative agents of acute gastroenteritis and a pressing public health burden worldwide. There are currently no vaccines or small molecule therapeutics available for the treatment or prophylaxis of norovirus infections. Norovirus 3CL protease plays a vital role in viral replication by generating structural and nonstructural proteins via the cleavage of the viral polyprotein ...

    Human noroviruses are the primary causative agents of acute gastroenteritis and a pressing public health burden worldwide. There are currently no vaccines or small molecule therapeutics available for the treatment or prophylaxis of norovirus infections. Norovirus 3CL protease plays a vital role in viral replication by generating structural and nonstructural proteins via the cleavage of the viral polyprotein. Thus, molecules that inhibit the viral protease may have potential therapeutic value. We describe herein the structure-based design, synthesis, and in vitro and cell-based evaluation of the first class of oxadiazole-based, permeable macrocyclic inhibitors of norovirus 3CL protease.


    Organizational Affiliation

    Department of Chemistry, Wichita State University , Wichita, Kansas 67260, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3C-LIKE PROTEASEA188Norovirus Hu/1968/USMutation(s): 0 
Gene Names: ORF1
EC: 3.4.22.66 (PDB Primary Data), 3.6.1.15 (UniProt), 2.7.7.48 (UniProt)
UniProt
Find proteins for Q83883 (Norwalk virus (strain GI/Human/United States/Norwalk/1968))
Explore Q83883 
Go to UniProtKB:  Q83883
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
V64 (Subject of Investigation/LOI)
Query on V64

Download Ideal Coordinates CCD File 
B [auth A]tert-butyl [(4S,7S,10S)-7-(cyclohexylmethyl)-10-(hydroxymethyl)-5,8,13-trioxo-22-oxa-6,9,14,20,21-pentaazabicyclo[17.2.1]docosa-1(21),19-dien-4-yl]carbamate
C29 H48 N6 O7
GGHACTZVDKMERX-FKBYEOEOSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.00 Å
  • R-Value Free: 0.154 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.143 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.169α = 90
b = 41.176β = 109.36
c = 61.679γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PHASERphasing
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 StatesR01 AI109039

Revision History  (Full details and data files)

  • Version 1.0: 2016-02-10
    Type: Initial release
  • Version 1.1: 2016-02-17
    Changes: Database references
  • Version 1.2: 2016-03-23
    Changes: Database references
  • Version 1.3: 2017-09-27
    Changes: Author supporting evidence, Database references, Derived calculations
  • Version 1.4: 2019-12-11
    Changes: Author supporting evidence
  • Version 1.5: 2020-08-12
    Changes: Structure summary