2MG8

Solution structure of TFF1 Estrogen Response Element complexed with DNA Bis-intercalating Anticancer Drug XR5944 (MLN944)

  • Classification: DNA
  • Mutation(s): No 

  • Deposited: 2013-10-30 Released: 2014-04-23 
  • Deposition Author(s): Lin, C.

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 14 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Solution structure of a 2:1 complex of anticancer drug XR5944 with TFF1 estrogen response element: insights into DNA recognition by a bis-intercalator.

Lin, C.Mathad, R.I.Zhang, Z.Sidell, N.Yang, D.

(2014) Nucleic Acids Res 42: 6012-6024

  • DOI: https://doi.org/10.1093/nar/gku219
  • Primary Citation of Related Structures:  
    2MG8

  • PubMed Abstract: 

    XR5944, a deoxyribonucleic acid (DNA) bis-intercalator with potent anticancer activity, can bind the estrogen response element (ERE) sequence to inhibit estrogen receptor-α activities. This novel mechanism of action may be useful for overcoming drug resistance to currently available antiestrogen treatments, all of which target the hormone-receptor complex. Here we report the nuclear magnetic resonance solution structure of the 2:1 complex of XR5944 with the naturally occurring TFF1-ERE, which exhibits important and unexpected features. In both drug-DNA complexes, XR5944 binds strongly at one intercalation site but weakly at the second site. The sites of intercalation within a native promoter sequence appear to be context and sequence dependent. The binding of one drug molecule influences the binding site of the second. Our structures underscore the fact that the DNA binding of a bis-intercalator is directional and different from the simple addition of two single intercalation sites. Our study suggests that improved XR5944 bis-intercalators targeting ERE may be designed through optimization of aminoalkyl linker and intercalation moieties at the weak binding sites.


  • Organizational Affiliation

    College of Pharmacy, University of Arizona, 1703 E. Mabel Street, Tucson, AZ 85721, USA.


Macromolecules

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Entity ID: 1
MoleculeChains LengthOrganismImage
5'-D(*AP*GP*GP*TP*CP*AP*CP*GP*GP*TP*GP*GP*CP*CP*A)-3'15N/A
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
5'-D(*TP*GP*GP*CP*CP*AP*CP*CP*GP*TP*GP*AP*CP*CP*T)-3'15N/A
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
XR2
Query on XR2

Download Ideal Coordinates CCD File 
C [auth B],
D [auth B]
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
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 14 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 2014-04-23 
  • Deposition Author(s): Lin, C.

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-23
    Type: Initial release
  • Version 1.1: 2014-06-04
    Changes: Database references
  • Version 1.2: 2014-09-17
    Changes: Other, Structure summary
  • Version 1.3: 2024-05-01
    Changes: Data collection, Database references, Derived calculations