6S15

Pyridine derivative of the natural alkaloid Berberine as Human Telomeric G-quadruplex Binder


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.266 
  • R-Value Observed: 0.268 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Pyridine Derivative of the Natural Alkaloid Berberine as Human Telomeric G4-DNA Binder: A Solution and Solid-State Study.

Papi, F.Bazzicalupi, C.Ferraroni, M.Ciolli, G.Lombardi, P.Khan, A.Y.Kumar, G.S.Gratteri, P.

(2020) ACS Med Chem Lett 11: 645-650

  • DOI: https://doi.org/10.1021/acsmedchemlett.9b00516
  • Primary Citation of Related Structures:  
    6S15

  • PubMed Abstract: 

    Telomerase is an enzyme deputed to the maintenance of eukaryotic chromosomes; however, its overexpression is a recognized hallmark of many cancer forms. A viable route for the inhibition of telomerase in malignant cells is the stabilization of G-quadruplex structures (G 4 ) at the 3' overhang of telomeres. Berberine has shown in this regard valuable G 4 binding properties together with a significant anticancer activity and telomerase inhibition effects. Here, we focused on a berberine derivative featuring a pyridine containing side group at the 13th position. Such modification actually improves the binding toward telomeric G-quadruplexes and establishes a degree of selectivity in the interaction with different sequences. Moreover, the X-ray crystal structure obtained for the complex formed by the ligand and a bimolecular human telomeric quadruplex affords a better understanding of the 13-berberine derivatives behavior with telomeric G 4 and allows to draw useful insights for the future design of derivatives with remarkable anticancer properties.


  • Organizational Affiliation

    Department of Chemistry 'Ugo Schiff', University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy.


Macromolecules

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
DNA TAGGGTTAGGGT
A, B
12synthetic construct
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.266 
  • R-Value Observed: 0.268 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.25α = 90
b = 41.25β = 90
c = 68.6γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-03
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description