6F60

The x-ray structure of bovine pancreatic ribonuclease in complex with a five-coordinate platinum(II) compound containing a sugar ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.14 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.138 
  • R-Value Observed: 0.141 

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This is version 1.0 of the entry. See complete history


Literature

Five-Coordinate Platinum(II) Compounds Containing Sugar Ligands: Synthesis, Characterization, Cytotoxic Activity, and Interaction with Biological Macromolecules.

Cucciolito, M.E.D'Amora, A.De Feo, G.Ferraro, G.Giorgio, A.Petruk, G.Monti, D.M.Merlino, A.Ruffo, F.

(2018) Inorg Chem 57: 3133-3143

  • DOI: https://doi.org/10.1021/acs.inorgchem.7b03118
  • Primary Citation of Related Structures:  
    6F60

  • PubMed Abstract: 

    This article describes the synthesis and characterization of novel cationic five-coordinate Pt(II) complexes containing nitrogen sugar-based ligands. The cytotoxicity of the complexes was evaluated on different cell lines with the expectation that both the coordinative saturation and the sugar moiety cooperate to enhance their biological activity. In fact, the complexes resulted to be more active than cisplatin but still with little selectivity. They activate the apoptosis pathway. Binding of representative compounds with DNA was studied by ethidium bromide displacement assay and circular dichroism. Binding to model proteins was also investigated; the X-ray structure of the adduct formed in the reaction between a representative compound and the model protein bovine pancreatic ribonuclease was obtained. The structure discloses an unprecedented interaction between a five-coordinate Pt(II) moiety and a His side chain.


  • Organizational Affiliation

    Dipartimento di Scienze Chimiche , Università di Napoli Federico II, Complesso Universitario di Monte S. Angelo , via Cintia 21 , 80126 Napoli , Italy.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribonuclease pancreatic
A, B
124Bos taurusMutation(s): 0 
EC: 3.1.27.5
UniProt
Find proteins for P61823 (Bos taurus)
Explore P61823 
Go to UniProtKB:  P61823
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61823
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DVW
Query on DVW

Download Ideal Coordinates CCD File 
D [auth A]five-coordinate platinum(II) compound
C27 H31 N7 O5 Pt
OIWCYKKCLNXBBS-UHFFFAOYSA-N
DW5
Query on DW5

Download Ideal Coordinates CCD File 
E [auth B]five-coordinate platinum(II) compound
C17 H15 N2 Pt
YTGODKYHPOIPHE-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.14 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.138 
  • R-Value Observed: 0.141 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.78α = 90
b = 32.519β = 90.19
c = 72.337γ = 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

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-25
    Type: Initial release