6MO0

Structure of dengue virus protease with an allosteric Inhibitor that blocks replication


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.311 
  • R-Value Work: 0.256 
  • R-Value Observed: 0.259 

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Ligand Structure Quality Assessment 


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Literature

Discovery, X-ray Crystallography and Antiviral Activity of Allosteric Inhibitors of Flavivirus NS2B-NS3 Protease.

Yao, Y.Huo, T.Lin, Y.L.Nie, S.Wu, F.Hua, Y.Wu, J.Kneubehl, A.R.Vogt, M.B.Rico-Hesse, R.Song, Y.

(2019) J Am Chem Soc 141: 6832-6836

  • DOI: 10.1021/jacs.9b02505
  • Primary Citation of Related Structures:  
    6MO1, 6MO0, 6MO2

  • PubMed Abstract: 
  • Flaviviruses, including dengue, West Nile and recently emerged Zika virus, are important human pathogens, but there are no drugs to prevent or treat these viral infections. The highly conserved Flavivirus NS2B-NS3 protease is essential for viral replication and therefore a drug target ...

    Flaviviruses, including dengue, West Nile and recently emerged Zika virus, are important human pathogens, but there are no drugs to prevent or treat these viral infections. The highly conserved Flavivirus NS2B-NS3 protease is essential for viral replication and therefore a drug target. Compound screening followed by medicinal chemistry yielded a series of drug-like, broadly active inhibitors of Flavivirus proteases with IC 50 as low as 120 nM. The inhibitor exhibited significant antiviral activities in cells (EC 68 : 300-600 nM) and in a mouse model of Zika virus infection. X-ray studies reveal that the inhibitors bind to an allosteric, mostly hydrophobic pocket of dengue NS3 and hold the protease in an open, catalytically inactive conformation. The inhibitors and their binding structures would be useful for rational drug development targeting Zika, dengue and other Flaviviruses.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
FLAVIVIRUS_NS2B/Peptidase S7A, B247Dengue virus 2Mutation(s): 0 
EC: 3.4.21.91 (UniProt), 3.6.1.15 (UniProt), 3.6.4.13 (UniProt)
UniProt
Find proteins for Q91H74 (Dengue virus 2)
Explore Q91H74 
Go to UniProtKB:  Q91H74
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JVJ (Subject of Investigation/LOI)
Query on JVJ

Download Ideal Coordinates CCD File 
C [auth A], D [auth B]1-(4-{3-[4-(furan-3-yl)phenyl]-5-[(piperidin-4-yl)methoxy]pyrazin-2-yl}phenyl)methanamine
C27 H28 N4 O2
NRQBIXPRZQFYDO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.311 
  • R-Value Work: 0.256 
  • R-Value Observed: 0.259 
  • Space Group: P 3 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.108α = 90
b = 109.108β = 90
c = 75.848γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentUnited StatesW81XWH-18-1-0368

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-22
    Type: Initial release