6XCL

Crystal Structure of human telomeric DNA G-quadruplex in complex with a novel platinum(II) complex.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report



Literature

Going Platinum to the Tune of a Remarkable Guanine Quadruplex Binder: Solution- and Solid-State Investigations.

Miron, C.E.van Staalduinen, L.Rangaswamy, A.M.M.Chen, M.Liang, Y.Jia, Z.Mergny, J.L.Petitjean, A.

(2020) Angew Chem Int Ed Engl 

  • DOI: 10.1002/anie.202012520
  • Primary Citation of Related Structures:  
    6XCL

  • PubMed Abstract: 
  • Guanine quadruplex recognition has gained increasing attention, inspired by the growing awareness of the key roles played by these non-canonical nucleic acid architectures in cellular regulatory processes. We report here the solution and solid-state ...

    Guanine quadruplex recognition has gained increasing attention, inspired by the growing awareness of the key roles played by these non-canonical nucleic acid architectures in cellular regulatory processes. We report here the solution and solid-state studies of a novel planar platinum(II) complex that is easily assembled from a simple ligand, and exhibits notable binding affinity for guanine quadruplex structures, while maintaining good selectivity for guanine quadruplex over duplex structures. A crystal structure of this ligand complexed with a telomeric quadruplex confirms double end-capping, with dimerization at the 5' interface.


    Organizational Affiliation

    Queen's University, Dept. of Chemistry, 90 Bader Lane, Chernoff Hall, K7L 3N6, Kingston, CANADA.



Macromolecules
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA (5'-D(*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*G)-3')A, B22Homo sapiens
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
V4A
Query on V4A

Download CCD File 
A, B
Platinum(II) bis[3-(pyridin-2-yl)-[1,2,4]triazolo[4,3-a]pyridine]
C22 H16 N8 Pt
RJNZXUGUJQBFMV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download CCD File 
A, B
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

Download CCD File 
A, B
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.194 
  • Space Group: P 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.03α = 90
b = 64.03β = 90
c = 42.23γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
MxDCdata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)Canada315311-2013

Revision History 

  • Version 1.0: 2020-11-04
    Type: Initial release