3CE5

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.213
R-Value Work: 0.183
R-Value Observed: 0.184

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1021/ja8016973
Primary Citation of 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

Organizational Affiliation

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

Macromolecule Content

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

Macromolecules

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(DTPDAPDGPDGPDGPDTPDTPDAPDGPDGPDGPDT)-3')	A, B	12	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BRA Query on BRA Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A]	E [auth A]	9-[4-(n,n-dimethylamino)phenylamino]-3,6-bis(3-pyrrolidinopropionamido) acridine C₃₅ H₄₃ N₇ O₂ RKPYSYRMIXRZJT-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
K Query on K Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A]	C [auth A], D [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.213
R-Value Work: 0.183
R-Value Observed: 0.184
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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-05-13

Deposition Author(s):

Revision History (Full details and data files)

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