6F6I

CRYSTAL STRUCTURE OF EBOLAVIRUS GLYCOPROTEIN IN COMPLEX WITH PAROXETINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Target Identification and Mode of Action of Four Chemically Divergent Drugs against Ebolavirus Infection.

Ren, J.Zhao, Y.Fry, E.E.Stuart, D.I.

(2018) J. Med. Chem. 61: 724-733

  • DOI: 10.1021/acs.jmedchem.7b01249
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Here we show that four chemically divergent approved drugs reported to inhibit Ebolavirus infection, benztropine, bepridil, paroxetine and sertraline, directly interact with the Ebolavirus glycoprotein. Binding of these drugs destabilise the protein, ...

    Here we show that four chemically divergent approved drugs reported to inhibit Ebolavirus infection, benztropine, bepridil, paroxetine and sertraline, directly interact with the Ebolavirus glycoprotein. Binding of these drugs destabilise the protein, suggesting that this may be the mechanism of inhibition, as reported for the anticancer drug toremifene and the painkiller ibuprofen, which bind in the same large cavity on the glycoprotein. Crystal structures show that the position of binding and the mode of interaction within the pocket vary significantly between these compounds. The binding constants (Kd) determined by thermal shift assay correlate with the protein-inhibitor interactions as well as with the antiviral activities determined by virus cell entry assays, supporting the hypothesis that these drugs inhibit viral entry by binding the glycoprotein and destabilising the pre-fusion conformation. Details of the protein-inhibitor interactions of these complexes and their relation with binding affinity may facilitate the design of more potent inhibitors.


    Related Citations: 
    • Toremifene interacts with and destabilizes the Ebola virus glycoprotein.
      Zhao, Y.,Ren, J.,Harlos, K.,Jones, D.M.,Zeltina, A.,Bowden, T.A.,Padilla-Parra, S.,Fry, E.E.,Stuart, D.I.
      (2016) Nature 535: 169



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Envelope glycoprotein,GP,GP1
A
330Zaire ebolavirus (strain Mayinga-76)Mutation(s): 1 
Gene Names: GP
Find proteins for Q05320 (Zaire ebolavirus (strain Mayinga-76))
Go to UniProtKB:  Q05320
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Envelope glycoprotein
B
168Zaire ebolavirus (strain Mayinga-76)Mutation(s): 1 
Gene Names: GP
Find proteins for Q05320 (Zaire ebolavirus (strain Mayinga-76))
Go to UniProtKB:  Q05320
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

Download SDF File 
Download CCD File 
B
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
B
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
8PR
Query on 8PR

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Download CCD File 
A
Paroxetine
(3S,4R)-3-[(1,3-benzodioxol-5-yloxy)methyl]-4-(4-fluorophenyl)piperidine
C19 H20 F N O3
AHOUBRCZNHFOSL-YOEHRIQHSA-N
 Ligand Interaction
DMS
Query on DMS

Download SDF File 
Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
A
L-PEPTIDE LINKINGC4 H9 N O2

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External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
8PRKd: 650000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.192 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 113.680α = 90.00
b = 113.680β = 90.00
c = 306.260γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data scaling
REFMACphasing
xia2data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
UKUnited KingdomMR/N00065X/1

Revision History 

  • Version 1.0: 2018-01-03
    Type: Initial release
  • Version 1.1: 2018-01-24
    Type: Database references
  • Version 1.2: 2018-02-21
    Type: Database references