3NYP

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

• PDB DOI: https://doi.org/10.2210/pdb3NYP/pdb
• NAKB: 3NYP

• Classification: DNA
• Mutation(s): No 


• Deposited: 2010-07-15 Released: 2010-08-25 
• Deposition Author(s): Campbell, N.H., Neidle, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.18 Å
• R-Value Free: 0.188 
• R-Value Work: 0.165 
• R-Value Observed: 0.166 

Literature

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.

(2011) Org Biomol Chem 9: 1328-1331

• PubMed: 21221451 
• DOI: https://doi.org/10.1039/c0ob00886a
• Primary Citation of Related Structures:  
  3NYP, 3NZ7


• PubMed Abstract: 
  

  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.

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Organizational Affiliation: 

The School of Pharmacy, University of London, 29-39 Brunswick Square, London, UK WC1N 1AX.

Biological Assembly 1  

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

Macromolecule Content

• Total Structure Weight: 8.26 kDa 
• Atom Count: 724 
• Modelled Residue Count: 24 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3'	A, B	12	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RNR	F [auth A]	3,6-bis(3-(3'-(R)-fluoropyrrolindino)propionamido)acridine C27 H31 F2 N5 O2 LWWRDCOEZPEHNJ-NHCUHLMSSA-N
K	C [auth A], D [auth A], E [auth A], G [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.18 Å
• R-Value Free: 0.188 
• R-Value Work: 0.165 
• R-Value Observed: 0.166 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.8	α = 90
b = 44.46	β = 90
c = 28.14	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-08-25 
Deposition Author(s): Campbell, N.H., Neidle, S.

Revision History  

• Version 1.0: 2010-08-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-11-16
  Changes: Atomic model
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description