Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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: 57.88 kDa 
• Atom Count: 3275 
• Residue Count: 381 
• Unique protein chains: 2

6G9B

Crystal structure of Ebolavirus glycoprotein in complex with imipramine

• DOI: 10.2210/pdb6G9B/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Ebola virus - Mayinga, Zaire, 1976
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2018-04-10 Released: 2018-05-23 
• Deposition Author(s): Zhao, Y., Ren, J., Fry, E.E., Xiao, J., Townsend, A.R., Stuart, D.I.
• Funding Organization(s): Medical Research Council (United Kingdom)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free: 0.225 
• R-Value Work: 0.196 
• R-Value Observed: 0.197 

Literature

Structures of Ebola Virus Glycoprotein Complexes with Tricyclic Antidepressant and Antipsychotic Drugs.

Zhao, Y., Ren, J., Fry, E.E., Xiao, J., Townsend, A.R., Stuart, D.I.

(2018) J Med Chem 61: 4938-4945

• PubMed: 29741894 
• DOI: 10.1021/acs.jmedchem.8b00350
• Primary Citation of Related Structures:  
  6G9B, 6G95, 6G9I


• PubMed Abstract: 
  

A large number of Food and Drug Administration (FDA)-approved drugs have been found to inhibit the cell entry of Ebola virus (EBOV). However, since these drugs have various primary pharmacological targets, their mechanisms of action against EBOV remain largely unknown. We have previously shown that six FDA-approved drugs inhibit EBOV infection by interacting with and destabilizing the viral glycoprotein (GP). Here we show that antidepressants imipramine and clomipramine and antipsychotic drug thioridazine also directly interact with EBOV GP and determine the mode of interaction by crystallographic analysis of the complexes. The compounds bind within the same pocket as observed for other, chemically divergent complexes but with different binding modes. These details should be of value for the development of potent EBOV inhibitors.

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Organizational Affiliation: 

Diamond Light Source Ltd , Harwell Science & Innovation Campus , Didcot OX11 0DE , U.K.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein,Envelope glycoprotein	A	330	Ebola virus - Mayinga, Zaire, 1976	Mutation(s): 1  Gene Names: GP
Find proteins for Q05320 (Zaire ebolavirus (strain Mayinga-76)) Explore Q05320  Go to UniProtKB:  Q05320

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein	B	168	Ebola virus - Mayinga, Zaire, 1976	Mutation(s): 1  Gene Names: GP
Find proteins for Q05320 (Zaire ebolavirus (strain Mayinga-76)) Explore Q05320  Go to UniProtKB:  Q05320

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	2		N-Glycosylation

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IXX	A, B	3-(5H-DIBENZO[B,F]AZEPIN-5-YL)-N,N-DIMETHYLPROPAN-1-AMINE C19 H24 N2 BCGWQEUPMDMJNV-UHFFFAOYSA-N
NAG	A	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL	A, B	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS	A, B	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
IXX	Kd:  584000   nM  Binding MOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free: 0.225 
• R-Value Work: 0.196 
• R-Value Observed: 0.197 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.216	α = 90
b = 114.216	β = 90
c = 305.552	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
xia2	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-04-10 
• Released Date: 2018-05-23 
Deposition Author(s): Zhao, Y., Ren, J., Fry, E.E., Xiao, J., Townsend, A.R., Stuart, D.I.

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Funding Organization	Location	Grant Number
Medical Research Council (United Kingdom)	United Kingdom	--

Revision History 

• Version 1.0: 2018-05-23
  Type: Initial release
  
• Version 1.1: 2018-06-27
  Changes: Data collection, Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary