9NNU | pdb_00009nnu

Crystal Structure of Ebola Envelope glycoprotein GP in complex with compound LD4-189ZbR

• PDB DOI: https://doi.org/10.2210/pdb9NNU/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Ebola virus - Mayinga, Zaire, 1976
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2025-03-06 Released: 2025-07-30 
• Deposition Author(s): Agrawal, S., Wilson, I.A.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free: 
  0.244 (Depositor), 0.237 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.219 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Starting Model: experimental

Literature

SuFEx-enabled high-throughput medicinal chemistry for developing potent tamoxifen analogs as Ebola virus entry inhibitors.

Dada, L., Nagai, E., Agrawal, S., Wirchnianski, A.S., Wilson, I.A., Chandran, K., Kitamura, S.

(2025) Front Immunol 16: 1533037-1533037

• PubMed: 40356906 
• DOI: https://doi.org/10.3389/fimmu.2025.1533037
• Primary Citation of Related Structures:  
  9NNU


• PubMed Abstract: 
  

  Ebola virus (EBOV) causes severe hemorrhagic fever with a high mortality rate in humans. In acute infection, an abnormal immune response results in excessive inflammatory cytokines and uncontrolled systemic inflammation that can result in organ damage and multi-organ failure. While vaccines and monoclonal antibody therapies are available, there is an urgent need for effective small-molecule antivirals against EBOV. Here, we report on the optimization of tamoxifen, an EBOV-glycoprotein (GP) binder that inhibits viral entry, using our Sulfur-Fluoride Exchange (SuFEx) click chemistry-based high-throughput medicinal chemistry (HTMC) strategy. Using a "Direct-to-Biology" approach, we generated a focused library of 2,496 tamoxifen analogs overnight and screened them in a cell-based pseudo-EBOV infection assay. The HTMC workflow enabled the development of a potent EBOV entry inhibitor with submicromolar EC ₅₀ cellular antiviral activity and more than 50-fold improvement in binding affinity against EBOV-GP compared to the parent compound. Our findings underscore the use of SuFEx-enabled HTMC for rapidly generating and assessing potential therapeutic candidates against viral and immune-mediated diseases in a cell-based assay.

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Organizational Affiliation: 
• Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, United States.
Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, United States.
Department of Microbiology & Immunology, Albert Einstein College of Medicine, Bronx, NY, United States.
Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 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)

Macromolecule Content 

• Total Structure Weight: 72.12 kDa 
• Atom Count: 3,006 
• Modeled Residue Count: 366 
• Deposited Residue Count: 638 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein	A	470	Ebola virus - Mayinga, Zaire, 1976	Mutation(s): 0  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
GP2	B	168	Ebola virus - Mayinga, Zaire, 1976	Mutation(s): 0  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	3D Interactions
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	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22573RC GlyCosmos:  G22573RC GlyGen:  G22573RC

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1BZF (Subject of Investigation/LOI)	H [auth A]	N-{3-[(1Z)-1-{4-[2-(dimethylamino)ethoxy]phenyl}-1-phenylbut-1-en-2-yl]phenyl}-N'-[(3R)-oxolan-3-yl]sulfuric diamide C30 H37 N3 O4 S TVWCPOPAZKQRCN-HDHBGBBSSA-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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free:  0.244 (Depositor), 0.237 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.219 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.222	α = 90
b = 114.222	β = 90
c = 306.37	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-30 
Deposition Author(s): Agrawal, S., Wilson, I.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History  

• Version 1.0: 2025-07-30
  Type: Initial release