5T6G

2.45 A resolution structure of Norovirus 3CL protease in complex with the dipeptidyl inhibitor 7m (hexagonal form)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure-based exploration and exploitation of the S4 subsite of norovirus 3CL protease in the design of potent and permeable inhibitors.

Galasiti Kankanamalage, A.C.Kim, Y.Rathnayake, A.D.Damalanka, V.C.Weerawarna, P.M.Doyle, S.T.Alsoudi, A.F.Dissanayake, D.M.Lushington, G.H.Mehzabeen, N.Battaile, K.P.Lovell, S.Chang, K.O.Groutas, W.C.

(2016) Eur J Med Chem 126: 502-516

  • DOI: 10.1016/j.ejmech.2016.11.027
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Human noroviruses are the primary cause of epidemic and sporadic acute gastroenteritis. The worldwide high morbidity and mortality associated with norovirus infections, particularly among the elderly, immunocompromised patients and children, constitu ...

    Human noroviruses are the primary cause of epidemic and sporadic acute gastroenteritis. The worldwide high morbidity and mortality associated with norovirus infections, particularly among the elderly, immunocompromised patients and children, constitute a serious public health concern. There are currently no approved human vaccines or norovirus-specific small-molecule therapeutics or prophylactics. Norovirus 3CL protease has recently emerged as a potential therapeutic target for the development of anti-norovirus agents. We hypothesized that the S4 subsite of the enzyme may provide an effective means of designing potent and cell permeable inhibitors of the enzyme. We report herein the structure-guided exploration and exploitation of the S4 subsite of norovirus 3CL protease in the design and synthesis of effective inhibitors of the protease.


    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
N40
Query on N40

Download SDF File 
Download CCD File 
A, B
3-cyclohexyl-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-N~2~-(octylsulfonyl)-L-alaninamide
3-cyclohexyl-N~2~-(octylsulfonyl)-N-{(2S)-1-oxo-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-alaninamide (bound form)
C24 H45 N3 O5 S
RZTXHLLGLPTYGI-FKBYEOEOSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.188 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 59.576α = 90.00
b = 59.576β = 90.00
c = 357.702γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata reduction
PDB_EXTRACTdata extraction
PHENIXrefinement
Aimlessdata scaling

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 StatesR01AI109039
National Institutes of Health/National Institute of General Medical SciencesUnited StatesP30GM110761

Revision History 

  • Version 1.0: 2016-11-23
    Type: Initial release
  • Version 1.1: 2017-01-11
    Type: Database references
  • Version 1.2: 2017-09-27
    Type: Author supporting evidence