Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Hetero 6-mer - A3B3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: homology

Macromolecule Content

• Total Structure Weight: 57780.57 
• Atom Count: 3217 
• Residue Count: 498 
• Unique protein chains: 2

6F6I

CRYSTAL STRUCTURE OF EBOLAVIRUS GLYCOPROTEIN IN COMPLEX WITH PAROXETINE

• DOI: 10.2210/pdb6F6I/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Zaire ebolavirus (strain Mayinga-76)
• Expression System: Homo sapiens
• Mutation(s): 2 


• Deposited: 2017-12-05 Released: 2018-01-03 
• Deposition Author(s): Ren, J., Zhao, Y., Fry, E.E., Stuart, D.I.
• Funding Organization(s): UK 

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Experimental Data Snapshot

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

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

• PubMed: 29272110 
• DOI: 10.1021/acs.jmedchem.7b01249
• Primary Citation of Related Structures:  
  6F6S, 6F6N, 6F5U


• 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, 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.

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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
Molecule	Chains	Sequence Length	Organism	Details
Envelope glycoprotein,GP,GP1	A	330	Zaire 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
Molecule	Chains	Sequence Length	Organism	Details
Envelope glycoprotein	B	168	Zaire 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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
GOL	A, B	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MAN	B	ALPHA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
BMA	B	BETA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-RWOPYEJCSA-N
8PR	A	Paroxetine (3S,4R)-3-[(1,3-benzodioxol-5-yloxy)methyl]-4-(4-fluorophenyl)piperidine C19 H20 F N O3 AHOUBRCZNHFOSL-YOEHRIQHSA-N
DMS	A	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
NAG	A, B	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
UNK	A	L-PEPTIDE LINKING	C4 H9 N O2		--

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
8PR	Kd: 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 = 113.680	α = 90.00
b = 113.680	β = 90.00
c = 306.260	γ = 120.00

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data scaling
REFMAC	phasing
xia2	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-12-05 
• Released Date: 2018-01-03 
• Deposition Author(s): Ren, J., Zhao, Y., Fry, E.E., Stuart, D.I.

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Funding Organization	Location	Grant Number
UK	United Kingdom	MR/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