1QV4

B-DNA Dodecamer CGTGAATTCACG complexed with minor groove binder methylproamine

  • Classification: DNA
  • Mutation(s): No 

  • Deposited: 2003-08-26 Released: 2004-09-07 
  • Deposition Author(s): Squire, C.J., Clark, G.R.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.220 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history. 


Literature

In vitro studies with methylproamine: a potent new radioprotector.

Martin, R.F., Broadhurst, S., Reum, M.E., Squire, C.J., Clark, G.R., Lobachevsky, P.N., White, J.M., Clark, C., Sy, D., Spotheim-Maurizot, M., Kelly, D.P.

(2004) Cancer Res 64: 1067-1070

  • DOI: https://doi.org/10.1158/0008-5472.can-03-2423
  • Primary Citation of Related Structures:  
    1QV4, 1QV8

  • PubMed Abstract: 

    New analogues of the minor groove binding ligand Hoechst 33342 have been investigated in an attempt to improve radioprotective activity. The synthesis, DNA binding, and in vitro radioprotective properties of methylproamine, the most potent derivative, are reported. Experiments with V79 cells have shown that methylproamine is approximately 100-fold more potent than the classical aminothiol radioprotector WR1065. The crystal structures of methylproamine and proamine complexes with the dodecamer d(CGCGAATTCGCG)(2) confirm that the new analogues also are minor groove binders. It is proposed that the DNA-bound methylproamine ligand acts as a reducing agent by an electron transfer mechanism, repairing transient radiation-induced oxidizing species on DNA.

    • Organizational Affiliation: 

    Trescowthick Research Laboratories, Peter MacCallum Cancer Centre, Melbourne, Australia.


Macromolecules

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'
A, B
12N/A
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MBB
Query on MBB
Download Ideal Coordinates CCD File 
C [auth B]2'-(3-METHYL-4-DIMETHYLAMINOPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE
C28 H31 N7
ADKLMOJIJGHCCD-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
MBB PDBBind:  1QV4 Kd: 124 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.220 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 25.44α = 90
b = 40.64β = 90
c = 66.35γ = 90
Software Package:
Software NamePurpose
Siemensdata collection
SAINTdata reduction
CNSrefinement
SMARTdata reduction
SAINTdata scaling
SADABSdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-09-07
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-03-07
    Changes: Data collection
  • Version 1.4: 2024-02-14
    Changes: Data collection, Database references, Derived calculations