3SC8

Crystal structure of an intramolecular human telomeric DNA G-quadruplex bound by the naphthalene diimide BMSG-SH-3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.302 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.258 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis for telomeric g-quadruplex targeting by naphthalene diimide ligands.

Collie, G.W.Promontorio, R.Hampel, S.M.Micco, M.Neidle, S.Parkinson, G.N.

(2012) J.Am.Chem.Soc. 134: 2723-2731

  • DOI: 10.1021/ja2102423
  • Primary Citation of Related Structures:  3T5E

  • PubMed Abstract: 
  • The folding of the single-stranded 3' end of the human telomere into G-quadruplex arrangements inhibits the overhang from hybridizing with the RNA template of telomerase and halts telomere maintenance in cancer cells. The ability to thermally stabili ...

    The folding of the single-stranded 3' end of the human telomere into G-quadruplex arrangements inhibits the overhang from hybridizing with the RNA template of telomerase and halts telomere maintenance in cancer cells. The ability to thermally stabilize human telomeric DNA as a four-stranded G-quadruplex structure by developing selective small molecule compounds is a therapeutic path to regulating telomerase activity and thereby selectively inhibit cancer cell growth. The development of compounds with the necessary selectivity and affinity to target parallel-stranded G-quadruplex structures has proved particularly challenging to date, relying heavily upon limited structural data. We report here on a structure-based approach to the design of quadruplex-binding ligands to enhance affinity and selectivity for human telomeric DNA. Crystal structures have been determined of complexes between a 22-mer intramolecular human telomeric quadruplex and two potent tetra-substituted naphthalene diimide compounds, functionalized with positively charged N-methyl-piperazine side-chains. These compounds promote parallel-stranded quadruplex topology, binding exclusively to the 3' surface of each quadruplex. There are significant differences between the complexes in terms of ligand mobility and in the interactions with quadruplex grooves. One of the two ligands is markedly less mobile in the crystal complex and is more quadruplex-stabilizing, forming multiple electrostatic/hydrogen bond contacts with quadruplex phosphate groups. The data presented here provides a structural rationale for the biophysical (effects on quadruplex thermal stabilization) and biological data (inhibition of proliferation in cancer cell lines and evidence of in vivo antitumor activity) on compounds in this series and, thus, for the concept of telomere targeting with DNA quadruplex-binding small molecules.


    Organizational Affiliation

    CRUK Biomolecular Structure Group, The School of Pharmacy, University of London, London, WC1N 1AX, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
Human telomeric repeat sequenceA22N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

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Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
R8G
Query on R8G

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Download CCD File 
A
2,7-bis[3-(4-methylpiperazin-1-yl)propyl]-4,9-bis{[3-(4-methylpiperazin-1-yl)propyl]amino}benzo[lmn][3,8]phenanthroline-1,3,6,8(2H,7H)-tetrone
C46 H72 N12 O4
KISMKSDSZPCOMD-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.302 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.258 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 50.870α = 90.00
b = 50.870β = 90.00
c = 52.460γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
GDAdata collection
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-02-15
    Type: Initial release
  • Version 1.1: 2012-02-22
    Type: Database references