5CCW

Structure of the complex of a human telomeric DNA with Au(caffein-2-ylidene)2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.225 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Determinants for Tight and Selective Binding of a Medicinal Dicarbene Gold(I) Complex to a Telomeric DNA G-Quadruplex: a Joint ESI MS and XRD Investigation.

Bazzicalupi, C.Ferraroni, M.Papi, F.Massai, L.Bertrand, B.Messori, L.Gratteri, P.Casini, A.

(2016) Angew.Chem.Int.Ed.Engl. 55: 4256-4259

  • DOI: 10.1002/anie.201511999

  • PubMed Abstract: 
  • The dicarbene gold(I) complex [Au(9-methylcaffein-8-ylidene)2 ]BF4 is an exceptional organometallic compound of profound interest as a prospective anticancer agent. This gold(I) complex was previously reported to be highly cytotoxic toward various ca ...

    The dicarbene gold(I) complex [Au(9-methylcaffein-8-ylidene)2 ]BF4 is an exceptional organometallic compound of profound interest as a prospective anticancer agent. This gold(I) complex was previously reported to be highly cytotoxic toward various cancer cell lines in vitro and behaves as a selective G-quadruplex stabilizer. Interactions of the gold complex with various telomeric DNA models have been analyzed by a combined ESI MS and X-ray diffraction (XRD) approach. ESI MS measurements confirmed formation of stable adducts between the intact gold(I) complex and Tel 23 DNA sequence. The crystal structure of the adduct formed between [Au(9-methylcaffein-8-ylidene)2 ](+) and Tel 23 DNA G-quadruplex was solved. Tel 23 maintains a characteristic propeller conformation while binding three gold(I) dicarbene moieties at two distinct sites. Stacking interactions appear to drive noncovalent binding of the gold(I) complex. The structural basis for tight gold(I) complex/G-quadruplex recognition and its selectivity are described.


    Organizational Affiliation

    Dipartimento di Chimica 'Ugo Schiff', UniversitĂ  degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, FI, Italy.




Macromolecules

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Entity ID: 1
MoleculeChainsLengthOrganism
human telomeric DNAA23Homo sapiens
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
51O
Query on 51O

Download SDF File 
Download CCD File 
A
Au(caffein-2-ylidene)2
C18 H24 Au N8 O4
SLZDDFRROPDGQR-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.225 
  • Space Group: I 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 47.129α = 90.00
b = 51.286β = 90.00
c = 58.768γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XSCALEdata scaling
XDSdata reduction
PDB_EXTRACTdata extraction
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-03-16
    Type: Initial release
  • Version 1.1: 2016-03-30
    Type: Database references