6KN4

HUMAN PARALLEL STRANDED 7-MER G-QUADRUPLEX COMPLEXED WITH 2 ADRIAMYCIN (DM2) MOLECULES


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 16 
  • Conformers Submitted: 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural basis for stabilization of human telomeric G-quadruplex [d-(TTAGGGT)]4by anticancer drug adriamycin.

Barthwal, R.Raje, S.Pandav, K.

(2020) J.Biomol.Struct.Dyn. --: 1-21

  • DOI: 10.1080/07391102.2020.1730969

  • PubMed Abstract: 
  • Besides inhibiting DNA duplication, DNA dependent RNA synthesis and topoisomerase-II enzyme action, anticancer drug adriamycin is found to cause telomere dysfunction and shows multiple strategies of action on gene functioning. We present evidence of ...

    Besides inhibiting DNA duplication, DNA dependent RNA synthesis and topoisomerase-II enzyme action, anticancer drug adriamycin is found to cause telomere dysfunction and shows multiple strategies of action on gene functioning. We present evidence of binding of adriamycin to parallel stranded intermolecular [d-(TTAGGGT)] 4 G-quadruplex DNA comprising human telomeric DNA by proton and phosphorus-31 nuclear magnetic resonance spectroscopy. Diffusion ordered spectroscopy shows formation of complex between the two molecules. Changes in chemical shift and line broadening of DNA and adriamycin protons suggest participation of specific chemical groups/moieties in interaction. Presence of sequential nuclear Overhauser enhancements at all base quartet steps and absence of large downfield shifts in 31 P resonances give clear proof of absence of intercalation of adriamycin chromophore between base quartets. Restrained molecular dynamics simulations using observed 15 short intermolecular inter proton distance contacts depict stacking of ring D of adriamycin with terminal G6 quartet by displacing T7 base and external groove binding close to T1-T2-A3 bases. The disappearance of imino protons monitored as a function of temperature and differential scanning calorimetry experiments yield thermal stabilization of 24 °C, which is likely to come in the way of telomerase association with telomeres. The findings pave the way for design of alternate anthracycline based drugs with specific modifications at ring D to enhance induced thermal stabilization and use alternate mechanism of binding to G-quadruplex DNA for interference in functional pathway of telomere maintenance by telomerase enzyme besides their well known action on duplex DNA.Communicated by Ramaswamy H. Sarma.


    Organizational Affiliation

    Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*(THM)P*TP*AP*GP*GP*GP*(TMP))-3')A,B,C,D7Homo sapiens
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DM2
Query on DM2

Download SDF File 
Download CCD File 
A
DOXORUBICIN
ADRIAMYCIN
C27 H29 N O11
AOJJSUZBOXZQNB-TZSSRYMLSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
TMP
Query on TMP
A, B, C, D
NON-POLYMERC10 H15 N2 O8 P

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THM
Query on THM
A, B, C, D
DNA OH 5 prime terminusC10 H14 N2 O5

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Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 16 
  • Conformers Submitted: 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-03-18
    Type: Initial release