3QSF

The first crystal structure of a human telomeric G-quadruplex DNA bound to a metal-containing ligand (a nickel complex)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.320 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.240 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Molecular basis of structure-activity relationships between salphen metal complexes and human telomeric DNA quadruplexes.

Campbell, N.H.Karim, N.H.Parkinson, G.N.Gunaratnam, M.Petrucci, V.Todd, A.K.Vilar, R.Neidle, S.

(2012) J Med Chem 55: 209-222

  • DOI: 10.1021/jm201140v
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The first X-ray crystal structures of nickel(II) and copper(II) salphen metal complexes bound to a quadruplex DNA are presented. Two structures have been determined and show that these salphen-metal complexes bind to human telomeric quadruplexes by e ...

    The first X-ray crystal structures of nickel(II) and copper(II) salphen metal complexes bound to a quadruplex DNA are presented. Two structures have been determined and show that these salphen-metal complexes bind to human telomeric quadruplexes by end-stacking, with the metal in each case almost in line with the potassium ion channel. Quadruplex and duplex DNA binding is presented for these two and other related salphen complexes, all with side-chains terminating in pyrrolidino end-groups and differing patterns of substitution on the salphen core. The crystal structures are able to provide rationalizations for the structure-activity data, and in particular for the superior quadruplex-binding of the nickel complexes compared to that of the copper-containing ones. The complexes show significant antiproliferative activity for the compounds in a panel of cancer cell lines. They also show telomerase inhibitory activity in the telomerase TRAP-LIG assay.


    Organizational Affiliation

    CRUK Biomolecular Structure Group, The School of Pharmacy, University of London, 29-29 Brunswick Square, London WC1N 1AX, U.K.



Macromolecules
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*T)-3'X12N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NUF
Query on NUF

Download CCD File 
X
[2,2'-{(4,5-difluorobenzene-1,2-diyl)bis[(nitrilo-kappaN)methylylidene]}bis{5-[2-(piperidin-1-yl)ethoxy]phenolato-kappa O}(2-)]nickel (II)
C34 H38 F2 N4 Ni O4
KYJUZDGNLQRIDM-OHUAMDITSA-L
 Ligand Interaction
K
Query on K

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.320 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.240 
  • Space Group: C 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.02α = 90
b = 54.909β = 90
c = 33.691γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-12-07
    Type: Initial release
  • Version 1.1: 2012-04-18
    Changes: Database references