4Z41 | pdb_00004z41

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 (Depositor), 0.231 (DCC) 
  • R-Value Work: 
    0.163 (Depositor), 0.173 (DCC) 
  • R-Value Observed: 
    0.166 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1021/acs.inorgchem.5b01238
  • Primary Citation Related Structures: 
    4Z3M, 4Z41

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 15.64 kDa 
  • Atom Count: 1,185 
  • Modeled Residue Count: 129 
  • Deposited Residue Count: 129 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Lysozyme C129Gallus gallusMutation(s): 0 
EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus)
Explore P00698 
Go to UniProtKB:  P00698
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00698
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
4KV

Query on 4KV



Download:Ideal Coordinates CCD File
B [auth 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
DMS

Query on DMS



Download:Ideal Coordinates CCD File
C [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
NO3

Query on NO3



Download:Ideal Coordinates CCD File
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
N [auth A]
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free:  0.219 (Depositor), 0.231 (DCC) 
  • R-Value Work:  0.163 (Depositor), 0.173 (DCC) 
  • R-Value Observed: 0.166 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.364α = 90
b = 78.364β = 90
c = 37.069γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2015-09-02
    Type: Initial release
  • Version 1.1: 2015-09-16
    Changes: Database references
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-10-16
    Changes: Structure summary