6GOH

X-ray structure of the adduct formed upon reaction of lysozyme with a Pt(II) complex bearing N,N-pyridylbenzimidazole derivative with an alkylated sulphonate side chain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.205 

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Literature

Exploring the interactions between model proteins and Pd(ii) or Pt(ii) compounds bearing charged N,N-pyridylbenzimidazole bidentate ligands by X-ray crystallography.

Ferraro, G.Mansour, A.M.Merlino, A.

(2018) Dalton Trans 47: 10130-10138

  • DOI: 10.1039/c8dt01663a
  • Primary Citation of Related Structures:  
    6GOB, 6GOH, 6GOI, 6GOJ, 6GOK

  • PubMed Abstract: 
  • Pd(ii) and Pt(ii) compounds bearing N,N-pyridylbenzimidazole derivatives with an alkylated sulfonate or phosphonium side chain are able to bind the model protein lysozyme both covalently and non-covalently as an entire compound or as a product of a hydrolysis reaction ...

    Pd(ii) and Pt(ii) compounds bearing N,N-pyridylbenzimidazole derivatives with an alkylated sulfonate or phosphonium side chain are able to bind the model protein lysozyme both covalently and non-covalently as an entire compound or as a product of a hydrolysis reaction. The interactions with the protein and the origin of the different behaviors of these complexes were unknown hitherto. Here, we present four crystal structures of their adducts with lysozyme. Pt- and Pd-containing fragments bind the protein with different stoichiometries close to the side chains of His15, Asp87, Asp101 and Asn77. The compounds bearing a phosphonium side chain degrade during the reaction with lysozyme. Data show the origin of the non-covalent mode of binding of Pd and Pt compounds bearing a sulfonate side chain, which drives the recognition process by forming a series of H-bonds and coulombic interactions with positively charged residue side chains. In a separate experiment, the structure of the adduct that is formed when the Pd(ii) compound containing an alkylated sulfonate group reacts with ribonuclease A was also determined. In this structure, the sulfonate-Pd(ii) complex binds the side chain of His105 on the surface of the protein and the side chain of the catalytically important His119 residue. Altogether, our data provide a structural basis for understanding the behavior of the analyzed Pd(ii)- and Pt(ii)-based cisplatin analogues in their reactions with proteins and show the first structural characterization of an adduct comprising a cisplatin analogue that is non-covalently bound to a protein. The results suggest that functionalization of a ligand system with a sulfonate group can significantly alter the protein-binding activity and thus the overall pharmacological profile of Pd(ii)- and Pt(ii)-based drugs.


    Organizational Affiliation

    Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, 80126 Napoli, Italy. antonello.merlino@unina.it.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Lysozyme CA129Gallus gallusMutation(s): 0 
Gene Names: LYZ
EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus)
Explore P00698 
Go to UniProtKB:  P00698
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
F7T (Subject of Investigation/LOI)
Query on F7T

Download Ideal Coordinates CCD File 
G [auth A], H [auth A]alkylated sulphonate-N,N-pyridylbenzimidazole-Pt complex
C15 H15 Cl2 N3 O3 Pt S
IZMHGJJPSRRFIR-UHFFFAOYSA-L
 Ligand Interaction
PT
Query on PT

Download Ideal Coordinates CCD File 
D [auth A], E [auth A]PLATINUM (II) ION
Pt
HRGDZIGMBDGFTC-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

Download Ideal Coordinates CCD File 
B [auth A], C [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
F [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.205 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.361α = 90
b = 78.361β = 90
c = 36.962γ = 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: 2018-07-25
    Type: Initial release
  • Version 1.1: 2018-08-08
    Changes: Data collection, Database references