3CE5 | pdb_00003ce5

A bimolecular parallel-stranded human telomeric quadruplex in complex with a 3,6,9-trisubstituted acridine molecule BRACO19

• PDB DOI: https://doi.org/10.2210/pdb3CE5/pdb
• NAKB: 3CE5

• Classification: DNA
• Mutation(s): No 


• Deposited: 2008-02-28 Released: 2008-05-13 
• Deposition Author(s): Campbell, N.H., Parkinson, G.N., Reszka, A.P., Neidle, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.213 (Depositor), 0.212 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.179 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

Structural basis of DNA quadruplex recognition by an acridine drug.

Campbell, N.H., Parkinson, G.N., Reszka, A.P., Neidle, S.

(2008) J Am Chem Soc 130: 6722-6724

• PubMed: 18457389 
• DOI: https://doi.org/10.1021/ja8016973
• Primary Citation Related Structures: 
  3CE5


• PubMed Abstract: 
  

  The crystal structure of a complex between the bimolecular human telomeric quadruplex d(TAGGGTTAGGGT)2 and the experimental anticancer drug BRACO-19, has been determined, to 2.5 A resolution. The binding site for the BRACO-19 molecule is at the interface of two parallel-folded quadruplexes, sandwiched between a G-tetrad surface and a TATA tetrad, and held in the site by networks of water molecules. The structure rationalizes the existing structure-activity data and provides a starting-point for the structure-based design of quadruplex-binding ligands

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Organizational Affiliation: 
• Cancer Research UK Biomolecular Structure Group, The School of Pharmacy, University of London, 29-39 Brunswick Square, London WC1N 1AX, United Kingdom.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 8.22 kDa 
• Atom Count: 605 
• Modeled Residue Count: 24 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 1

Macromolecules

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BRA	E [auth A]	9-[4-(n,n-dimethylamino)phenylamino]-3,6-bis(3-pyrrolidinopropionamido) acridine C35 H43 N7 O2 RKPYSYRMIXRZJT-UHFFFAOYSA-N
K	C [auth A], D [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.213 (Depositor), 0.212 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.179 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.338	α = 90
b = 70.338	β = 90
c = 34.293	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-05-13 
Deposition Author(s): Campbell, N.H., Parkinson, G.N., Reszka, A.P., Neidle, S.

Revision History  

• Version 1.0: 2008-05-13
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-01-11
  Changes: Other
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description