5LIG

G-Quadruplex formed at the 5'-end of NHEIII_1 Element in human c-MYC promoter bound to triangulenium based fluorescence probe DAOTA-M2


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the least restraint violations 

wwPDB Validation 3D Report Full Report


This is version 2.1 of the entry. See complete history

Literature

NMR Structure of a Triangulenium-Based Long-Lived Fluorescence Probe Bound to a G-Quadruplex.

Kotar, A.Wang, B.Shivalingam, A.Gonzalez-Garcia, J.Vilar, R.Plavec, J.

(2016) Angew.Chem.Int.Ed.Engl. 55: 12508-12511

  • DOI: 10.1002/anie.201606877

  • PubMed Abstract: 
  • An NMR structural study of the interaction between a small-molecule optical probe (DAOTA-M2) and a G-quadruplex from the promoter region of the c-myc oncogene revealed that they interact at 1:2 binding stoichiometry. NMR-restrained structural calcula ...

    An NMR structural study of the interaction between a small-molecule optical probe (DAOTA-M2) and a G-quadruplex from the promoter region of the c-myc oncogene revealed that they interact at 1:2 binding stoichiometry. NMR-restrained structural calculations show that binding of DAOTA-M2 occurs mainly through π-π stacking between the polyaromatic core of the ligand and guanine residues of the outer G-quartets. Interestingly, the binding affinities of DAOTA-M2 differ by a factor of two for the outer G-quartets of the unimolecular parallel G-quadruplex under study. Unrestrained MD calculations indicate that DAOTA-M2 displays significant dynamic behavior when stacked on a G-quartet plane. These studies provide molecular guidelines for the design of triangulenium derivatives that can be used as optical probes for G-quadruplexes.


    Organizational Affiliation

    Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia.,Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, Ljubljana, Slovenia. Janez.plavec@ki.si.,Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia. Janez.plavec@ki.si.,Department of Chemistry, Imperial College London, South Kensington, London, SW7 2AZ, UK.,EN-FIST Center of Excellence, Trg OF 13, 1000, Ljubljana, Slovenia. Janez.plavec@ki.si.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*AP*GP*GP*GP*AP*GP*GP*GP*TP*AP*GP*GP*GP*AP*GP*GP*GP*T)-3')A19Homo sapiens
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6XM
Query on 6XM

Download SDF File 
Download CCD File 
A
8,12-bis(2-morpholinoethyl)-8H-benzo[ij]xantheno[1,9,8-cdef][2,7]naphthyridin-12-iumhexafluorophosphate
C31 H34 N4 O3
JDODSALIMITEDK-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the least restraint violations 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Slovenian Research AgencySloveniaP1-242
Slovenian Research AgencySloveniaJ1-6733

Revision History 

  • Version 1.0: 2016-09-14
    Type: Initial release
  • Version 1.1: 2016-09-28
    Type: Database references
  • Version 1.2: 2018-02-14
    Type: Data collection
  • Version 2.0: 2018-03-07
    Type: Advisory, Atomic model, Derived calculations, Non-polymer description
  • Version 2.1: 2019-05-08
    Type: Data collection