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

• PDB DOI: https://doi.org/10.2210/pdb3EUI/pdb
• NAKB: 3EUI

• Classification: DNA
• Mutation(s): No 


• Deposited: 2008-10-10 Released: 2008-12-02 
• Deposition Author(s): Campbell, N.H., Parkinson, G., Neidle, S.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.285 
• R-Value Work: 0.234 
• R-Value Observed: 0.237 

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

• PubMed: 19173611 
• DOI: https://doi.org/10.1021/bi802233v
• Primary Citation of Related Structures:  
  3EM2, 3EQW, 3ERU, 3ES0, 3ET8, 3EUI, 3EUM


• 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 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.

Biological Assembly 1  

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 16.82 kDa 
• Atom Count: 1,276 
• Modelled Residue Count: 48 
• Deposited Residue Count: 48 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*DGP*DGP*DGP*DGP*DTP*DTP*DTP*DTP*DGP*DGP*DGP*DG)-3'	A, B, C, D	12	N/A

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NCI	N [auth C]	3,6-Bis{3-[(2R)-(2-ethylpiperidino)]propionamido}acridine C33 H45 N5 O2 ZWPUGYBFVBXUSX-FQLXRVMXSA-N
NC5	H [auth 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
SPM	J [auth B]	SPERMINE C10 H26 N4 PFNFFQXMRSDOHW-UHFFFAOYSA-N
K	E [auth A], F [auth A], G [auth A], I [auth B], K [auth C], L [auth C], M [auth C], O [auth D]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.285 
• R-Value Work: 0.234 
• R-Value Observed: 0.237 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.356	α = 90
b = 42.542	β = 90
c = 48.636	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
PHASER	phasing
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-12-02 
Deposition Author(s): Campbell, N.H., Parkinson, G., Neidle, S.

Revision History  

• Version 1.0: 2008-12-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2018-04-04
  Changes: Data collection
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description