1QDA

Crystal structure of epidoxorubicin-formaldehyde virtual crosslink of DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Crystal structure of epidoxorubicin-formaldehyde virtual crosslink of DNA and evidence for its formation in human breast-cancer cells.

Podell, E.R.Harrington, D.J.Taatjes, D.J.Koch, T.H.

(1999) Acta Crystallogr.,Sect.D 55: 1516-1523


  • PubMed Abstract: 
  • Epidoxorubicin and daunorubicin are proposed to be cytotoxic to tumor cells by catalyzing production of formaldehyde through redox cycling and using the formaldehyde for covalent attachment to DNA at G bases. The crystal structure of epidoxorubicin c ...

    Epidoxorubicin and daunorubicin are proposed to be cytotoxic to tumor cells by catalyzing production of formaldehyde through redox cycling and using the formaldehyde for covalent attachment to DNA at G bases. The crystal structure of epidoxorubicin covalently bound to a d(CGCGCG) oligomer was determined to 1.6 A resolution. The structure reveals slightly distorted B-form DNA bearing two molecules of epidoxorubicin symmetrically intercalated at the termini, with each covalently attached from its N3' to N2 of a G base via a CH2 group from the formaldehyde. The structure is analogous to daunorubicin covalently bound to d(CGCGCG) determined previously, except for additional hydrogen bonding from the epimeric O4' to O2 of a C base. The role of drug-DNA covalent bonding in cells was investigated with synthetic epidoxorubicin-formaldehyde conjugate (Epidoxoform) and synthetic daunorubicin-formaldehyde conjugate (Daunoform). Uptake and location of drug fluorophore in doxorubicin-resistant human breast-cancer cells (MCF-7/ADR cells) was observed by fluorescence microscopy and flow cytometry. The fluorophore of Daunoform appeared more rapidly in cells and was released more rapidly from cells than the fluorophore of Epidoxoform over a 3 h exposure period. The fluorophore appeared predominantly in the nucleus of cells treated with both conjugates. The difference in uptake is explained in terms of the slower rate of hydrolysis of Epidoxoform to the species reactive with DNA and a proposed slower release from DNA based upon the crystal structures.


    Related Citations: 
    • A redox pathway leading to the alkylation of nucleic acids by doxorubicin and related anthracyclines: application to the design of antitumor drugs for resistant cancer.
      Taatjes, D.J.,Fenick, D.J.,Gaudiano, G.,Koch, T.H.
      (1998) Curr.Pharm.Des. 4: 203
    • Epidoxoform: A Hydrolytically More Stable Anthracycline-Formaldehyde Conjugate Toxic to Resistant Tumor Cells
      Taatjes, D.J.,Fenick, D.J.,Koch, T.H.
      (1998) J.Med.Chem. 41: 2452


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0215, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
5' -D(CP*GP*CP*(G49)P*CP*GP)-3'A6N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DM6
Query on DM6

Download SDF File 
Download CCD File 
A
4'-EPIDOXORUBICIN
4'-EPIADRIAMYCIN
C27 H30 N O11
AOJJSUZBOXZQNB-VTZDEGQISA-O
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
G49
Query on G49
A
DNA LINKINGC11 H16 N5 O7 PDG
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.205 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 28.110α = 90.00
b = 28.110β = 90.00
c = 52.540γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
CNSrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-09-15
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2014-03-12
    Type: Database references
  • Version 1.4: 2017-10-04
    Type: Refinement description