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 

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


  • 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 proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
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
K
Query on K

Download SDF File 
Download CCD File 
A, B
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
PYN
Query on PYN

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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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.139 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 55.451α = 90.00
b = 42.736β = 90.00
c = 26.926γ = 90.00
Software Package:
Software NamePurpose
EPMRphasing
SCALEPACKdata scaling
SHELXL-97refinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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