6FC9

The 1,8-bis(aminomethyl)anthracene and Quadruplex-duplex junction complex


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 20 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

De Novo Design of Selective Quadruplex-Duplex Junction Ligands and Structural Characterisation of Their Binding Mode: Targeting the G4 Hot-Spot.

Diaz-Casado, L.Serrano-Chacon, I.Montalvillo-Jimenez, L.Corzana, F.Bastida, A.Santana, A.G.Gonzalez, C.Asensio, J.L.

(2020) Chemistry 

  • DOI: https://doi.org/10.1002/chem.202005026
  • Primary Citation of Related Structures:  
    6FC9

  • PubMed Abstract: 

    Targeting the interface between DNA quadruplex and duplex regions by small molecules holds significant promise in both therapeutics and nanotechnology. Herein, a new pharmacophore is reported, which selectively binds with high affinity to quadruplex-duplex junctions, while presenting a poorer affinity for G-quadruplex or duplex DNA alone. Ligands complying with the reported pharmacophore exhibit a significant affinity and selectivity for quadruplex-duplex junctions, including the one observed in the HIV-1 LTR-III sequence. The structure of the complex between a quadruplex-duplex junction with a ligand of this family has been determined by NMR methods. According to these data, the remarkable selectivity of this structural motif for quadruplex-duplex junctions is achieved through an unprecedented interaction mode so far unexploited in medicinal and biological chemistry: the insertion of a benzylic ammonium moiety into the centre of the partially exposed G-tetrad at the interface with the duplex. Further decoration of the described scaffolds with additional fragments opens up the road to the development of selective ligands for G-quadruplex-forming regions of the genome.


  • Organizational Affiliation

    Glycochemistry and Molecular Recognition group-Dpt. Bio-Organic Chemistry, Instituto de Química Orgánica General (IQOG-CSIC), Juan de la Cierva 3., 28006, Madrid, Spain.


Macromolecules
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (27-MER)27synthetic construct
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
D5B
Query on D5B

Download Ideal Coordinates CCD File 
B [auth A][8-(azaniumylmethyl)anthracen-1-yl]methylazanium
C16 H18 N2
NTFMELQYTBAEQP-UHFFFAOYSA-P
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 20 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-10
    Type: Initial release
  • Version 1.1: 2019-05-08
    Changes: Data collection
  • Version 1.2: 2021-04-07
    Changes: Data collection, Database references
  • Version 1.3: 2023-06-14
    Changes: Database references, Other
  • Version 1.4: 2024-06-19
    Changes: Data collection, Database references