7Z9L

Phen-DC3 intercalation causes hybrid-to-antiparallel transformation of human telomeric DNA G-quadruplex

• PDB DOI: https://doi.org/10.2210/pdb7Z9L/pdb
• NAKB: 7Z9L
• BMRB: 34714

• Classification: DNA
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2022-03-21 Released: 2022-08-31 
• Deposition Author(s): Ghosh, A., Trajkovski, M., Teulade-Fichou, M.P., Gabelica, V., Plavec, J.
• Funding Organization(s): European Union (EU), Slovenian Research Agency, Foundation for Medical Research (France)

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Literature

Phen-DC 3 Induces Refolding of Human Telomeric DNA into a Chair-Type Antiparallel G-Quadruplex through Ligand Intercalation.

Ghosh, A., Trajkovski, M., Teulade-Fichou, M.P., Gabelica, V., Plavec, J.

(2022) Angew Chem Int Ed Engl 61: e202207384-e202207384

• PubMed: 35993443 
• DOI: https://doi.org/10.1002/anie.202207384
• Primary Citation of Related Structures:  
  7Z9L


• PubMed Abstract: 
  

  Human telomeric G-quadruplex DNA structures are attractive anticancer drug targets, but the target's polymorphism complicates the drug design: different ligands prefer different folds, and very few complexes have been solved at high resolution. Here we report that Phen-DC ₃ , one of the most prominent G-quadruplex ligands in terms of high binding affinity and selectivity, causes dTAGGG(TTAGGG) ₃ to completely change its fold in KCl solution from a hybrid-1 to an antiparallel chair-type structure, wherein the ligand intercalates between a two-quartet unit and a pseudo-quartet, thereby ejecting one potassium ion. This unprecedented high-resolution NMR structure shows for the first time a true ligand intercalation into an intramolecular G-quadruplex.

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Organizational Affiliation: 

CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, Université de Bordeaux, 33600, Pessac, France.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: NMR Distance Restraints

Macromolecule Content

• Total Structure Weight: 7.84 kDa 
• Atom Count: 527 
• Modelled Residue Count: 23 
• Deposited Residue Count: 23 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*G)-3')	A	23	Homo sapiens

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PQ3 (Subject of Investigation/LOI)	B [auth A]	N2,N9-bis(1-methylquinolin-3-yl)-1,10-phenanthroline-2,9-dicarboxamide C34 H26 N6 O2 TXHVLDXCHPTTDG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-08-31 
Deposition Author(s): Ghosh, A., Trajkovski, M., Teulade-Fichou, M.P., Gabelica, V., Plavec, J.

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Funding Organization	Location	Grant Number
European Union (EU)	European Union	799695
Slovenian Research Agency	Slovenia	P1-0242
Slovenian Research Agency	Slovenia	J1-1704
Foundation for Medical Research (France)	France	DCM20181039571

Revision History  

• Version 1.0: 2022-08-31
  Type: Initial release
  
• Version 1.1: 2022-09-07
  Changes: Database references
• Version 1.2: 2022-09-14
  Changes: Database references
• Version 1.3: 2022-10-05
  Changes: Database references