3EUI

A bimolecular anti-parallel-stranded Oxytricha nova telomeric quadruplex in complex with a 3,6-disubstituted acridine BSU-6042 in a large unit cell


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.234 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Selectivity in Ligand Recognition of G-Quadruplex Loops.

Campbell, N.H.Patel, M.Tofa, A.B.Ghosh, R.Parkinson, G.N.Neidle, S.

(2009) Biochemistry 48: 1675-1680

  • DOI: 10.1021/bi802233v
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • A series of disubstituted acridine ligands have been cocrystallized with a bimolecular DNA G-quadruplex. The ligands have a range of cyclic amino end groups of varying size. The crystal structures show that the diagonal loop in this quadruplex result ...

    A series of disubstituted acridine ligands have been cocrystallized with a bimolecular DNA G-quadruplex. The ligands have a range of cyclic amino end groups of varying size. The crystal structures show that the diagonal loop in this quadruplex results in a large cavity for these groups, in contrast to the steric constraints imposed by propeller loops in human telomeric quadruplexes. We conclude that the nature of the loop has a significant influence on ligand selectivity for particular quadruplex folds.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*DGP*DGP*DGP*DGP*DTP*DTP*DTP*DTP*DGP*DGP*DGP*DG)-3'A,B,C,D12N/A
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

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

Download SDF File 
Download CCD File 
B
SPERMINE
C10 H26 N4
PFNFFQXMRSDOHW-UHFFFAOYSA-N
 Ligand Interaction
NCI
Query on NCI

Download SDF File 
Download CCD File 
C
3,6-Bis{3-[(2R)-(2-ethylpiperidino)]propionamido}acridine
N,N'-acridine-3,6-diylbis{3-[(2R)-2-ethylpiperidin-1-yl]propanamide}
C33 H45 N5 O2
ZWPUGYBFVBXUSX-FQLXRVMXSA-N
 Ligand Interaction
NC5
Query on NC5

Download SDF File 
Download CCD File 
A
3-[(2R)-2-ethylpiperidin-1-yl]-N-[6-({3-[(2S)-2-ethylpiperidin-1-yl]propanoyl}amino)acridin-3-yl]propanamide
C33 H45 N5 O2
ZWPUGYBFVBXUSX-ISILISOKSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.234 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 55.356α = 90.00
b = 42.542β = 90.00
c = 48.636γ = 90.00
Software Package:
Software NamePurpose
d*TREKdata reduction
REFMACrefinement
CrystalCleardata collection
d*TREKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-12-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2018-04-04
    Type: Data collection