4BZU

The Solution Structure of the MLN 944-d(TATGCATA)2 Complex


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 
  • Conformers Submitted: 
  • Selection Criteria: DISTANCE RESTRAINTS 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The Solution Structure of Bis(Phenazine-1-Carboxamide)-DNA Complexes: Mln 944 Binding Corrected and Extended.

Serobian, A.Thomas, D.S.Ball, G.E.Denny, W.A.Wakelin, L.P.G.

(2014) Biopolymers 101: 1099

  • DOI: 10.1002/bip.22513
  • Primary Citation of Related Structures:  4BZT, 4BZV

  • PubMed Abstract: 
  • MLN 944 is a bisintercalating DNA-binding antitumor agent known to be a template inhibitor of transcription. Previous (1) H NMR studies of its d(ATGCAT)2 complex concluded that its phenazine chromophores are protonated. However, we find that this is ...

    MLN 944 is a bisintercalating DNA-binding antitumor agent known to be a template inhibitor of transcription. Previous (1) H NMR studies of its d(ATGCAT)2 complex concluded that its phenazine chromophores are protonated. However, we find that this is not so, which has important consequences for the charged state of the ligand, for the orientation of its 1-carboxamide group in the complex, and for the details of the interaction of its protonated interchromophore linker with the DNA base pairs. Here, we report a corrected solution structure of the MLN 944-d(ATGCAT)2 complex, and extend the study to complexes with d(TATGCATA)2 , and d(TACGCGTA)2 , using a variety of (1) H and (31) P NMR methods and molecular dynamics simulations employing the AMBER 12 force field. We find that for all three complexes MLN 944 binds as a dication, in which the chromophores are uncharged, in the DNA major groove spanning the central 2 GC base pairs in a manner that maintains the dyad symmetry of the DNA. The carboxamide group lies in the plane of the chromophore, its NH making hydrogen bonding interactions with the phenazine N10 nitrogen, and the protonated linkers form hydrogen bonds with the O6 atom of guanine. The dynamics simulations reveal extensive solvent interactions involving the linker amines, the carboxamide group, and the DNA bases.


    Organizational Affiliation

    Department of Pharmacology, School of Medical Sciences, Faculty of Medicine, UNSW Australia, Sydney, 2052, NSW, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNAA,B8synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
XR2
Query on XR2

Download SDF File 
Download CCD File 
A
1-METHYL-9-[12-(9-METHYLPHENAZIN-10-IUM-1-YL)-12-OXO-2,11-DIAZA-5,8-DIAZONIADODEC-1-ANOYL]PHENAZIN-10-IUM
C34 H38 N8 O2
SFOADSRLCHRTKT-UHFFFAOYSA-R
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 
  • Conformers Submitted: 
  • Selection Criteria: DISTANCE RESTRAINTS 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-08-21
    Type: Initial release
  • Version 1.1: 2013-08-28
    Type: Structure summary
  • Version 1.2: 2013-09-04
    Type: Structure summary
  • Version 1.3: 2014-09-03
    Type: Database references