3EUI | pdb_00003eui

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 (Depositor), 0.280 (DCC)
R-Value Work:
0.234 (Depositor), 0.230 (DCC)
R-Value Observed:
0.237 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 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

PubMed: 19173611 Search on PubMed
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.

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

Find similar nucleic acids by: Sequence | 3D Structure

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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NCI Query on NCI Download Ideal Coordinates CCD File SDF format, chain N [auth C] MOL2 format, chain N [auth C] mmCIF format, chain N [auth C]	N [auth C]	3,6-Bis{3-[(2R)-(2-ethylpiperidino)]propionamido}acridine C₃₃ H₄₅ N₅ O₂ ZWPUGYBFVBXUSX-FQLXRVMXSA-N		Interactions Focus chain N [auth C] Interactions & Density Focus chain N [auth C]
NC5 Query on NC5 Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	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		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
SPM Query on SPM Download Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B] mmCIF format, chain J [auth B]	J [auth B]	SPERMINE C₁₀ H₂₆ N₄ PFNFFQXMRSDOHW-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]
K Query on K Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain K [auth C] SDF format, chain L [auth C] SDF format, chain M [auth C] SDF format, chain O [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] MOL2 format, chain O [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain K [auth C] mmCIF format, chain L [auth C] mmCIF format, chain M [auth C] mmCIF format, chain O [auth D]	E [auth A] F [auth A] G [auth A] I [auth B] K [auth C] 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		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Focus chain O [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Focus chain O [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.285 (Depositor), 0.280 (DCC)
R-Value Work: 0.234 (Depositor), 0.230 (DCC)
R-Value Observed: 0.237 (Depositor)

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

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-12-02

Deposition Author(s):

Campbell, N.H.

Parkinson, G.

Neidle, S.

Revision History (Full details and data files)

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

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