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: 58.49 kDa 
• Atom Count: 3416 
• Residue Count: 388 
• Unique protein chains: 2

6HS4

Crystal structure of Ebolavirus glycoprotein in complex with inhibitor 118

• DOI: 10.2210/pdb6HS4/pdb

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


• Deposited: 2018-09-28 Released: 2019-02-27 
• Deposition Author(s): Ren, J., Zhao, Y., Stuart, D.I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.220 
• R-Value Work: 0.190 
• R-Value Observed: 0.192 

Literature

Structure-Based in Silico Screening Identifies a Potent Ebolavirus Inhibitor from a Traditional Chinese Medicine Library.

Shaikh, F., Zhao, Y., Alvarez, L., Iliopoulou, M., Lohans, C., Schofield, C.J., Padilla-Parra, S., Siu, S.W.I., Fry, E.E., Ren, J., Stuart, D.I.

(2019) J Med Chem 62: 2928-2937

• PubMed: 30785281 
• DOI: 10.1021/acs.jmedchem.8b01328
• Primary Citation of Related Structures:  
  6HS4, 6HRO


• PubMed Abstract: 
  

Potent Ebolavirus (EBOV) inhibitors will help to curtail outbreaks such as that which occurred in 2014-16 in West Africa. EBOV has on its surface a single glycoprotein (GP) critical for viral entry and membrane fusion. Recent high-resolution complexes of EBOV GP with a variety of approved drugs revealed that binding to a common cavity prevented fusion of the virus and endosomal membranes, inhibiting virus infection. We performed docking experiments, screening a database of natural compounds to identify those likely to bind at this site. Using both inhibition assays of HIV-1-derived pseudovirus cell entry and structural analyses of the complexes of the compounds with GP, we show here that two of these compounds attach in the common binding cavity, out of eight tested. In both cases, two molecules bind in the cavity. The two compounds are chemically similar, but the tighter binder has an additional chlorine atom that forms good halogen bonds to the protein and achieves an IC ₅₀ of 50 nM, making it the most potent GP-binding EBOV inhibitor yet identified, validating our screening approach for the discovery of novel antiviral compounds.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein,GP1,Envelope glycoprotein	A	331	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
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	5		N-Glycosylation

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GON	A	1-[2-[3-oxidanyl-4-(4-phenyl-1~{H}-pyrazol-5-yl)phenoxy]ethyl]piperidine-4-carboxamide C23 H26 N4 O3 PYIQTHALSLWYHD-UHFFFAOYSA-N
NAG	A, B	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	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
GON	IC50:  3100   nM  Binding MOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.220 
• R-Value Work: 0.190 
• R-Value Observed: 0.192 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.16	α = 90
b = 114.16	β = 90
c = 305.458	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2018-09-28 
• Released Date: 2019-02-27 
Deposition Author(s): Ren, J., Zhao, Y., Stuart, D.I.

Revision History 

• Version 1.0: 2019-02-27
  Type: Initial release
  
• Version 1.1: 2019-04-10
  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