1L1H

Crystal Structure of the Quadruplex DNA-Drug Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.139 
  • R-Value Observed: 0.144 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of a G-quadruplex-Ligand Complex

Haider, S.M.Parkinson, G.N.Neidle, S.

(2003) J Mol Biol 326: 117-125

  • DOI: 10.1016/s0022-2836(02)01354-2
  • Primary Citation of Related Structures:  
    1L1H

  • PubMed Abstract: 
  • Stabilisation of G-quadruplex structures formed from telomeric DNA, by means of quadruplex-selective ligands, is a means of inhibiting the telomerase enzyme from catalysing the synthesis of telomeric DNA repeats. In order to understand the molecular ...

    Stabilisation of G-quadruplex structures formed from telomeric DNA, by means of quadruplex-selective ligands, is a means of inhibiting the telomerase enzyme from catalysing the synthesis of telomeric DNA repeats. In order to understand the molecular basis of ligand-quadruplex recognition, the crystal structure has been determined of such a complex, at 1.75A resolution. This complex is between a dimeric antiparallel G-quadruplex formed from the Oxytricha nova telomeric DNA sequence d(GGGGTTTTGGGG), and a di-substituted aminoalkylamido acridine compound. The structure shows that the acridine moiety is bound at one end of the stack of G-quartets, within one of the thymine loops. It is held in place by a combination of stacking interactions and specific hydrogen bonds with thymine bases. The stability of the ligand in this binding site has been confirmed by a 2ns molecular dynamics simulation.


    Organizational Affiliation

    Cancer Research UK Biomolecular Structure Group, The School of Pharmacy, University of London, 29-39 Brunswick Square, WC1N 1AX, London, UK.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3'A, B12N/A
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    PYN
    Query on PYN

    Download CCD File 
    A
    3-PYRROLIDIN-1-YL-N-[6-(3-PYRROLIDIN-1-YL-PROPIONYLAMINO)-ACRIDIN-3-YL]-PROPIONAMIDE
    C27 H33 N5 O2
    WQSTTZVZUNIDBE-UHFFFAOYSA-N
     Ligand Interaction
    K
    Query on K

    Download CCD File 
    A, B
    POTASSIUM ION
    K
    NPYPAHLBTDXSSS-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.75 Å
    • R-Value Free: 0.219 
    • R-Value Work: 0.139 
    • R-Value Observed: 0.144 
    • Space Group: P 21 21 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 55.451α = 90
    b = 42.736β = 90
    c = 26.926γ = 90
    Software Package:
    Software NamePurpose
    DENZOdata reduction
    SCALEPACKdata scaling
    EPMRphasing
    SHELXL-97refinement

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2003-02-11
      Type: Initial release
    • Version 1.1: 2008-04-28
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance