2WPU

Chaperoned ruthenium metallodrugs that recognize telomeric DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Chemo-Genetic Optimization of DNA Recognition by Metallodrugs Using a Presenter-Protein Strategy.

Zimbron, J.M.Sardo, A.Heinisch, T.Wohlschlager, T.Gradinaru, J.Massa, C.Schirmer, T.Creus, M.Ward, T.R.

(2010) Chemistry 16: 12883

  • DOI: 10.1002/chem.201001573

  • PubMed Abstract: 
  • The mode of action of precious metal anticancer metallodrugs is generally believed to involve DNA as a target. However, the poor specificity of such drugs often requires high doses and leads to undesirable side-effects. With the aim of improving the ...

    The mode of action of precious metal anticancer metallodrugs is generally believed to involve DNA as a target. However, the poor specificity of such drugs often requires high doses and leads to undesirable side-effects. With the aim of improving the specificity of a ruthenium piano-stool complex towards DNA, we employed a presenter protein strategy based on the biotin-avidin technology. Guided by the X-ray structure of the assembly of streptavidin and a biotinylated piano-stool, we explored the formation of metallodrug-mediated ternary complexes with the presenter protein and DNA. The assemblies bound more strongly to telomere G-quadruplexes than to double-stranded DNA; chemo-genetic modifications (varying the complex or mutating the protein) modulated binding to these targets. We suggest that rational targeting of small molecules by presenter proteins could be exploited to bind metallodrugs to preferred macromolecular targets.


    Organizational Affiliation

    University of Basel, Department of Chemistry, Spitalstrasse 51, 4056 Basel, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
STREPTAVIDIN
A
159Streptomyces avidiniiMutation(s): 0 
Find proteins for P22629 (Streptomyces avidinii)
Go to UniProtKB:  P22629
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
KYT
Query on KYT

Download SDF File 
Download CCD File 
A
(3AS,4S,6AR)-4-(5-((3R,4R)-3,4-DIAMINOPYRROLIDIN-1-YL)-5-OXOPENTYL)TETRAHYDRO-1H-THIENO[3,4-D]IMIDAZOL-2(3H)-ONE-P-CYMENE-CHLORO-RUTHENIUM(III)
C24 H39 Cl N5 O2 Ru S
OJIBJWGHGYGDGX-SNKMZJELSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
KYTKd: <60 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.172 
  • Space Group: I 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 57.680α = 90.00
b = 57.680β = 90.00
c = 183.694γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
MOSFLMdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-10-13
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2019-01-30
    Type: Data collection, Experimental preparation, Other
  • Version 1.4: 2019-02-06
    Type: Data collection, Experimental preparation