7Z9L

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


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


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

  • 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.


  • Organizational Affiliation

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


Macromolecules

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
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')23Homo sapiens
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PQ3 (Subject of Investigation/LOI)
Query on PQ3

Download Ideal Coordinates CCD File 
B [auth A]N2,N9-bis(1-methylquinolin-3-yl)-1,10-phenanthroline-2,9-dicarboxamide
C34 H26 N6 O2
CTOLNXAGCUTHBW-UHFFFAOYSA-P
Experimental Data & Validation

Experimental Data

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

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Union (EU)European Union799695
Slovenian Research AgencySloveniaP1-0242
Slovenian Research AgencySloveniaJ1-1704
Foundation for Medical Research (France)FranceDCM20181039571

Revision History  (Full details and data files)

  • 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
  • Version 2.0: 2024-05-15
    Changes: Data collection, Database references, Non-polymer description