6BID

1.15 A resolution structure of Norovirus 3CL protease in complex with a triazole-based macrocyclic inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.143 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

Putative structural rearrangements associated with the interaction of macrocyclic inhibitors with norovirus 3CL protease.

Galasiti Kankanamalage, A.C.Weerawarna, P.M.Rathnayake, A.D.Kim, Y.Mehzabeen, N.Battaile, K.P.Lovell, S.Chang, K.O.Groutas, W.C.

(2019) Proteins 87: 579-587

  • DOI: 10.1002/prot.25682
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Human noroviruses are the primary cause of outbreaks of acute gastroenteritis worldwide. The problem is further compounded by the current lack of norovirus-specific antivirals or vaccines. Noroviruses have a single-stranded, positive sense 7 to 8 kb ...

    Human noroviruses are the primary cause of outbreaks of acute gastroenteritis worldwide. The problem is further compounded by the current lack of norovirus-specific antivirals or vaccines. Noroviruses have a single-stranded, positive sense 7 to 8 kb RNA genome which encodes a polyprotein precursor that is processed by a virus-encoded 3C-like cysteine protease (NV 3CLpro) to generate at least six mature nonstructural proteins. Processing of the polyprotein is essential for virus replication, consequently, NV 3CLpro has emerged as an attractive target for the discovery of norovirus therapeutics and prophylactics. We have recently described the structure-based design of macrocyclic transition state inhibitors of NV 3CLpro. In order to gain insight and understanding into the interaction of macrocyclic inhibitors with the enzyme, as well as probe the effect of ring size on pharmacological activity and cellular permeability, additional macrocyclic inhibitors were synthesized and high resolution cocrystal structures determined. The results of our studies tentatively suggest that the macrocyclic scaffold may hamper optimal binding to the active site by impeding concerted cross-talk between the S 2 and S 4 subsites.


    Organizational Affiliation

    Department of Chemistry, Wichita State University, Kansas.,Protein Structure Laboratory, The University of Kansas, Kansas.,Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Kansas.,IMCA-CAT, Hauptman-Woodward Medical Research Institute, APS Argonne National Laboratory, Argonne, Illinois.




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
DW4
Query on DW4

Download SDF File 
Download CCD File 
A
benzyl [(8S,11S,14S)-11-(cyclohexylmethyl)-8-(hydroxymethyl)-5,10,13-trioxo-1,4,9,12,17,18-hexaazabicyclo[14.2.1]nonadeca-16(19),17-dien-14-yl]carbamate
C29 H41 N7 O6
QPOBCHAUHXOWOC-HVCNVCAESA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.143 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 66.107α = 90.00
b = 39.394β = 108.56
c = 61.454γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PHASERphasing
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 Diseases (NIH/NIAID)United StatesAI109039
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP30GM110761

Revision History 

  • Version 1.0: 2018-11-07
    Type: Initial release
  • Version 1.1: 2018-12-12
    Type: Data collection, Source and taxonomy
  • Version 1.2: 2019-02-20
    Type: Author supporting evidence, Data collection
  • Version 1.3: 2019-04-03
    Type: Data collection, Database references
  • Version 1.4: 2019-06-12
    Type: Data collection, Database references
  • Version 1.5: 2019-12-11
    Type: Author supporting evidence