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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Ligand Structure Quality Assessment 


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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: 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 ...

    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

    Consorzio Interuniversitario di Reattività Chimica e Catalisi (CIRCC) , via Celso Ulpiani 27 , 70126 Bari , Italy.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ribonuclease pancreaticA, B124Bos taurusMutation(s): 0 
Gene Names: RNASE1RNS1
EC: 3.1.27.5 (PDB Primary Data), 4.6.1.18 (UniProt)
UniProt
Find proteins for P61823 (Bos taurus)
Explore P61823 
Go to UniProtKB:  P61823
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DVW (Subject of Investigation/LOI)
Query on DVW

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

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

Download Ideal Coordinates CCD File 
C [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
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