8PH7

X-ray structure of the adduct formed upon reaction of Lysozyme with [Ru2Cl(DPhF)(O2CCH3)3] in condition A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.226 

Starting Model: experimental
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Literature

Steric hindrance and charge influence on the cytotoxic activity and protein binding properties of diruthenium complexes.

Teran, A.Ferraro, G.Imbimbo, P.Sanchez-Pelaez, A.E.Monti, D.M.Herrero, S.Merlino, A.

(2023) Int J Biol Macromol 253: 126666-126666

  • DOI: https://doi.org/10.1016/j.ijbiomac.2023.126666
  • Primary Citation of Related Structures:  
    8PH5, 8PH6, 8PH7, 8PH8

  • PubMed Abstract: 

    Paddlewheel diruthenium complexes are being used as metal-based drugs. It has been proposed that their charge and steric properties determine their selectivity towards proteins. Here, we explore these parameters using the first water-soluble diruthenium complex bearing two formamidinate ligands, [Ru 2 Cl(DPhF) 2 (O 2 CCH 3 ) 2 ], and two derivatives, [Ru 2 Cl(DPhF)(O 2 CCH 3 ) 3 ] and K 2 [Ru 2 (DPhF)(CO 3 ) 3 ] (DPhF -  = N,N'-diphenylformamidinate), with one formamidinate. Their protein binding properties have been assessed employing hen egg white lysozyme (HEWL). The results confirm the relationship between the type of interaction (coordinate/non-coordinate bonds) and the charge of diruthenium complexes. The crystallization medium is also a key factor. In all cases, diruthenium species maintain the M-M bond and produce stable adducts. The antiproliferative properties of these diruthenium complexes have been evaluated on an eukaryotic cell-based model. Our data show a correlation between the number of the formamidinate ligands and the anticancer activity of the diruthenium derivatives against human epithelial carcinoma cells. Increased cytotoxicity may be related to increased steric hindrance and Ru 2 5+ core electronic density. However, the effect of increasing the lipophilicity of diruthenium species by introducing a second N,N'-diphenylformamidinate must be also considered. This work illustrates a systematic approach to shed light on the relevant properties of diruthenium compounds to design metal-based metallodrugs and diruthenium metalloenzymes.


  • Organizational Affiliation

    MatMoPol Research Group, Department of Inorganic Chemistry, Faculty of Chemical Sciences, Complutense University of Madrid, Avda. Complutense s/n, 28040 Madrid, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  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
ZWH
Query on ZWH

Download Ideal Coordinates CCD File 
D [auth A][Ru2Cl(N,N'-bis(4-fluorophenyl)formamidinate)(1,1-ethanediol)(succinic acid)2]
C23 H28 N2 O10 Ru2
GPMJGBXYFGQHON-UHFFFAOYSA-N
ZQ2 (Subject of Investigation/LOI)
Query on ZQ2

Download Ideal Coordinates CCD File 
B [auth A][Ru2(N,N'-bis(4-fluorophenyl)formamidinate)(1,1-ethanediol)
C15 H16 N2 O2 Ru2
HYYYEFNDCLICTP-UHFFFAOYSA-N
SIN (Subject of Investigation/LOI)
Query on SIN

Download Ideal Coordinates CCD File 
C [auth A]SUCCINIC ACID
C4 H6 O4
KDYFGRWQOYBRFD-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
E [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.226 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.67α = 90
b = 77.67β = 90
c = 38.28γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-09-13
    Type: Initial release
  • Version 1.1: 2023-09-20
    Changes: Database references
  • Version 1.2: 2024-10-23
    Changes: Structure summary