8QN2 | pdb_00008qn2

Helical foldamers as selective G-quadruplex ligands

• PDB DOI: https://doi.org/10.2210/pdb8QN2/pdb
• NAKB: 8QN2

• Classification: GENE REGULATION
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2023-09-25 Released: 2025-04-09 
• Deposition Author(s): Koenig, A., Thore, S., Gabelica, V.
• Funding Organization(s): Agence Nationale de la Recherche (ANR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free: 
  0.308 (Depositor), 0.309 (DCC) 
• R-Value Work: 
  0.272 (Depositor), 0.270 (DCC) 
• R-Value Observed: 
  0.276 (Depositor) 

Starting Model: experimental

Literature

Helical aromatic oligoamide foldamers as selective G-quadruplex ligands

Koenig, A., Laffile, V., Largy, E., Thore, S., Mackereth, C., Ferrand, Y., Gabelica, V.

(2025) Nucleic Acids Res 

• DOI: https://doi.org/10.1093/nar/gkaf1365

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: NMR Distance Restraints

Macromolecule Content 

• Total Structure Weight: 8.32 kDa 
• Atom Count: 531 
• Modeled Residue Count: 30 
• Deposited Residue Count: 30 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ACE-QUK-QUK-ZY9-QUK	B, C	5	synthetic construct	Mutation(s): 0

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*T)-3')	A	20	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K	D [auth A], E [auth A], F [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG	G [auth A], H [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free:  0.308 (Depositor), 0.309 (DCC) 
• R-Value Work:  0.272 (Depositor), 0.270 (DCC) 
• R-Value Observed: 0.276 (Depositor) 

Space Group: P 4₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.71	α = 90
b = 32.71	β = 90
c = 61.01	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-04-09 
Deposition Author(s): Koenig, A., Thore, S., Gabelica, V.

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Funding Organization	Location	Grant Number
Agence Nationale de la Recherche (ANR)	France	ANR-18-CE29-0013 POLYnESI

Revision History  

• Version 1.0: 2025-04-09
  Type: Initial release
  
• Version 1.1: 2025-12-17
  Changes: Database references