6MO0 | pdb_00006mo0

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 (Depositor), 0.308 (DCC) 
  • R-Value Work: 
    0.256 (Depositor), 0.279 (DCC) 
  • R-Value Observed: 
    0.259 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

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: https://doi.org/10.1021/jacs.9b02505
  • Primary Citation Related Structures: 
    6MO0, 6MO1, 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. 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.

Macromolecule Content 

  • Total Structure Weight: 53.54 kDa 
  • Atom Count: 2,578 
  • Modeled Residue Count: 328 
  • Deposited Residue Count: 494 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
FLAVIVIRUS_NS2B/Peptidase S7
A, B
247dengue virus type 2Mutation(s): 0 
UniProt
Find proteins for A0A0B4L2Y4 (Dengue virus type 2)
Explore A0A0B4L2Y4 
Go to UniProtKB:  A0A0B4L2Y4
Find proteins for Q91H74 (Dengue virus type 2)
Explore Q91H74 
Go to UniProtKB:  Q91H74
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ91H74A0A0B4L2Y4
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
JVJ

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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.311 (Depositor), 0.308 (DCC) 
  • R-Value Work:  0.256 (Depositor), 0.279 (DCC) 
  • R-Value Observed: 0.259 (Depositor) 
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

View Full Validation Report



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
  • Version 1.1: 2023-10-11
    Changes: Data collection, Database references, Refinement description