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Structure of the First Parallel DNA Quadruplex-drug Complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.17 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Structure of the First Parallel DNA Quadruplex-drug Complex

Clark, G.R., Pytel, P.D., Squire, C.J., Neidle, S.

(2003) J.Am.Chem.Soc. 125: 4066-4067

  • DOI: 10.1021/ja0297988

  • PubMed Abstract: 

    • The first crystal structure of a drug (daunomycin) bound to a parallel-stranded intermolecular telomeric G4 quadruplex (d(TGGGGT)4) has been determined to high resolution. A planar assemblage of three daunomycin molecules stacks onto the 5' end of th ...

    The first crystal structure of a drug (daunomycin) bound to a parallel-stranded intermolecular telomeric G4 quadruplex (d(TGGGGT)4) has been determined to high resolution. A planar assemblage of three daunomycin molecules stacks onto the 5' end of the G4 column, with the daunosamine substituents occupying three of the four quadruplex grooves. The surface area of the terminal G-quartet in this parallel DNA quadruplex, presently occupied by three daunomycins, is sufficiently large that it could easily accommodate other potential telomerase inhibitors such as substituted porphyrins or telomestatin.

    Organizational Affiliation: 

    Department of Chemistry, University of Auckland, Auckland, New Zealand. g.clark@auckland.ac.nz




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*TP*GP*GP*GP*GP*T)-3'A,B,C,D6N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DM1
Query on DM1
Download SDF File 
Download CCD File 
B, C, D
DAUNOMYCIN
DAUNORUBICIN
C27 H29 N O10
STQGQHZAVUOBTE-VGBVRHCVSA-N
 Ligand Interaction
NA
Query on NA
Download SDF File 
Download CCD File 
A, C
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.17 Å
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 53.004α = 90.00
b = 47.073β = 119.80
c = 31.865γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
AMoREphasing
SHELXL-97refinement
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-04-15
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance