4Z41

X-ray structure of the adduct formed in the reaction between lysozyme and a platinum(II) Compound with a S,O Bidentate Ligand (9a=Chloro-(1-(3'-hydroxy)-3-(methylthio)-3-thioxo-prop-1-en-1-olate-O,S)-(dimethylsulfoxide-S)-platinum(II))

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Platinum(II) Complexes with O,S Bidentate Ligands: Biophysical Characterization, Antiproliferative Activity, and Crystallographic Evidence of Protein Binding.

Mugge, C., Marzo, T., Massai, L., Hildebrandt, J., Ferraro, G., Rivera-Fuentes, P., Metzler-Nolte, N., Merlino, A., Messori, L., Weigand, W.

(2015) Inorg.Chem. 54: 8560-8570

  • DOI: 10.1021/acs.inorgchem.5b01238
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • We recently characterized a series of novel platinum(II) compounds bearing a conserved O,S binding moiety as a bifunctional ligand and evaluated their solution behavior and antiproliferative properties in vitro against a representative cancer cell li ...

    We recently characterized a series of novel platinum(II) compounds bearing a conserved O,S binding moiety as a bifunctional ligand and evaluated their solution behavior and antiproliferative properties in vitro against a representative cancer cell line. On the whole, those platinum compounds showed an appreciable stability in mixed dimethyl sulfoxide-aqueous buffers and promising in vitro cytotoxic effects; yet they manifested a rather limited solubility in aqueous media making them poorly suitable for further pharmaceutical development. To overcome this drawback, four new derivatives of this series were prepared and characterized based on a careful choice of substituents on the O,S bidentate ligand. The solubility and stability profile of these novel compounds in a reference buffer was determined, as well as the ligands' log P(o/w) value (P(o/w) = n-octanol-water partition coefficient) as an indirect measure for the complexes' lipophilicity. The antiproliferative properties were comparatively evaluated in a panel of three cancer cell lines. The protein binding properties of the four platinum compounds were assessed using the model protein hen egg white lysozyme (HEWL), and the molecular structures of two relevant HEWL-metallodrug adducts were solved. Overall, it is shown that a proper choice of the substituents leads to a higher solubility and enables a selective fine-tuning of the antiproliferative properties. The implications of these results are thoroughly discussed.

    Organizational Affiliation: 

    Institute of Inorganic and Analytical Chemistry, Friedrich-Schiller-University Jena , Humboldtstraße 8, 07743 Jena, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysozyme C
A
129Gallus gallusGene Names: LYZ
EC: 3.2.1.17
Find proteins for P00698 (Gallus gallus)
Go to Gene View: LYZ
Go to UniProtKB:  P00698
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO
Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
4KV
Query on 4KV
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Download CCD File 
A
3-[2-chloranyl-2-[dimethyl(oxidanyl)-{4}-sulfanyl]-4-ethylsulfanyl-1-oxa-3{3}-thia-2{4}-platinacyclohexa-3,5-dien-6-yl]phenol
C13 H18 Cl O3 Pt S3
WTWNXRGJOPEVSJ-SULXSYCDSA-L
 Ligand Interaction
DMS
Query on DMS
Download SDF File 
Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
NO3
Query on NO3
Download SDF File 
Download CCD File 
A
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.163 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 78.364α = 90.00
b = 78.364β = 90.00
c = 37.069γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2015-04-01 
  • Released Date: 2015-09-02 
  • Deposition Author(s): Merlino, A.

Revision History 

  • Version 1.0: 2015-09-02
    Type: Initial release
  • Version 1.1: 2015-09-16
    Type: Database references