ISDA: 3NYP

Deposition Date 2010-07-15

Release Date 2010-08-25

Last Version Date 2023-09-06

Entry Detail

PDB ID:

3NYP

Keywords:

DNA

Title:

A bimolecular anti-parallel-stranded Oxytricha nova telomeric quadruplex in complex with a 3,6-disubstituted acridine ligand containing bis-3-fluoropyrrolidine end side chains

Biological Source:

Source Organism:

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

1.18 Å

R-Value Free:

0.18

R-Value Work:

0.16

R-Value Observed:

0.16

Space Group:

P 21 21 2

Download Validation Report

Macromolecular Entities

Polymer Type:polydeoxyribonucleotide
Molecule:5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3'
Chain IDs:A, B
Chain Length:12
Number of Molecules:2
Biological Source:

Ligand Molecules

RNR

Primary Citation

Fluorine in medicinal chemistry: beta-fluorination of peripheral pyrrolidines attached to acridine ligands affects their interactions with G-quadruplex DNA.

Campbell, N.H, Smith, D.L, Reszka, A.P, Neidle, S, O'Hagan, D.Show

Org.Biomol.Chem. 9 1328 1331 (2011)

PMID: 21221451 DOI: 10.1039/c0ob00886a

Abstact

Comparative X-ray structure studies reveal that C-F bond incorporation into the peripheral pyrrolidine moieties of the G-quadruplex DNA binding ligand BSU6039 leads to a distinct pyrrolidine ring conformation, relative to the non-fluorinated analogue, and with a different binding mode involving reversal of the pyrrolidinium N(+)-H orientation.

Legend

Protein

Chemical

Disease

Primary Citation of related structures