6NAE | pdb_00006nae

Crystal Structure of Ebola zaire GP protein with bound ARN0074898

• PDB DOI: https://doi.org/10.2210/pdb6NAE/pdb

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


• Deposited: 2018-12-05 Released: 2019-12-11 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 
  0.240 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

Discovery of Adamantane Carboxamides as Ebola Virus Cell Entry and Glycoprotein Inhibitors.

Plewe, M.B., Sokolova, N.V., Gantla, V.R., Brown, E.R., Naik, S., Fetsko, A., Lorimer, D.D., Dranow, D.M., Smutney, H., Bullen, J., Sidhu, R., Master, A., Wang, J., Kallel, E.A., Zhang, L., Kalveram, B., Freiberg, A.N., Henkel, G., McCormack, K.

(2020) ACS Med Chem Lett 11: 1160-1167

• PubMed: 32550996 
• DOI: https://doi.org/10.1021/acsmedchemlett.0c00025
• Primary Citation Related Structures: 
  6NAE


• PubMed Abstract: 
  

  We identified and explored the structure-activity-relationship (SAR) of an adamantane carboxamide chemical series of Ebola virus (EBOV) inhibitors. Selected analogs exhibited half-maximal inhibitory concentrations (EC ₅₀ values) of ∼10-15 nM in vesicular stomatitis virus (VSV) pseudotyped EBOV (pEBOV) infectivity assays, low hundred nanomolar EC ₅₀ activity against wild type EBOV, aqueous solubility >20 mg/mL, and attractive metabolic stability in human and nonhuman liver microsomes. X-ray cocrystallographic characterizations of a lead compound with the EBOV glycoprotein (GP) established the EBOV GP as a target for direct compound inhibitory activity and further provided relevant structural models that may assist in identifying optimized therapeutic candidates.

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Organizational Affiliation: 
• Arisan Therapeutics, 11189 Sorrento Valley Road, Suite 104, San Diego, California 92121, United States.
Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98105, United States.
UCB Pharma, 7869 NE Day Road West, Bainbridge Island, Washington 98110, United States.
UCB Pharma, 3 Preston Court, Bedford, Massachusetts 01730, United States.
Victrix, 12631 Bendito Drive, San Diego, California 92128, United States.
Department of Pathology andCenter for Biodefense and Emerging Infectious Diseases, The University of Texas Medical Branch, Galveston, Texas 77555, United States.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 57.85 kDa 
• Atom Count: 2,972 
• Modeled Residue Count: 355 
• Deposited Residue Count: 498 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein,Envelope glycoprotein,Envelope glycoprotein	A	330	Ebola virus - Mayinga, Zaire, 1976	Mutation(s): 1  Gene Names: GP
UniProt
Find proteins for Q05320 (Zaire ebolavirus (strain Mayinga-76)) Explore Q05320  Go to UniProtKB:  Q05320
Glycosylation
Glycosylation Sites: 4

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
UniProt
Find proteins for Q05320 (Zaire ebolavirus (strain Mayinga-76)) Explore Q05320  Go to UniProtKB:  Q05320
Glycosylation
Glycosylation Sites: 1

Oligosaccharides

Help  

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
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
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
KHG	K [auth A]	(1S,3R,5R,7S)-N-(trans-4-aminocyclohexyl)-3-methyl-5-phenyltricyclo[3.3.1.1~3,7~]decane-1-carboxamide C24 H34 N2 O TZNRCHUCVIMHIH-UCWUHLBISA-N
NAG	D [auth A], E [auth A], F [auth A], G [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL	H [auth A], I [auth A], J [auth A], L [auth A], M [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free:  0.240 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m36nae

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.25	α = 90
b = 113.25	β = 90
c = 307.21	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-12-11 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2019-12-11
  Type: Initial release
  
• Version 1.1: 2019-12-25
  Changes: Database references
• Version 1.2: 2020-07-01
  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
• Version 2.1: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
• Version 2.2: 2024-11-20
  Changes: Structure summary