5E5F | pdb_00005e5f

X-ray structure of the complex between RNase A and compound 4-PF6 ([(PPh3)Au(mi-pbi)Pt(Me)(DMSO)][PF6]), the heterobimetallic derivative obtained in the reaction between the organometallic compound [Pt(pbi)(Me)(DMSO)], pbi=2-(2'-pyridil)benzimidazole (compound 3) and the gold(I) compound [Au(Ph3P)][PF6]

• PDB DOI: https://doi.org/10.2210/pdb5E5F/pdb

• Classification: HYDROLASE
• Organism(s): Bos taurus
• Mutation(s): No 


• Deposited: 2015-10-08 Released: 2015-12-09 
• Deposition Author(s): Merlino, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free: 
  0.234 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Literature

Cytotoxic properties of a new organometallic platinum(ii) complex and its gold(i) heterobimetallic derivatives.

Serratrice, M., Maiore, L., Zucca, A., Stoccoro, S., Landini, I., Mini, E., Massai, L., Ferraro, G., Merlino, A., Messori, L., Cinellu, M.A.

(2015) Dalton Trans 45: 579-590

• PubMed: 26609781 
• DOI: https://doi.org/10.1039/c5dt02714d
• Primary Citation Related Structures: 
  5E5E, 5E5F


• PubMed Abstract: 
  

  A novel platinum(ii) organometallic complex, [Pt(pbi)(Me)(DMSO)], bearing the 2-(2'-pyridyl)-benzimidazole (pbiH) ligand, was synthesized and fully characterized. Interestingly, the reaction of this organometallic platinum(ii) complex with two distinct gold(i) phosphane compounds afforded the corresponding heterobimetallic derivatives with the pbi ligand bridging the two metal centers. The antiproliferative properties in vitro of [Pt(pbi)(Me)(DMSO)] and its gold(i) derivatives as well as those of the known coordination platinum(ii) and palladium(ii) complexes with the same ligand, of the general formula [MCl2(pbiH)], were comparatively evaluated against A2780 cancer cells, either sensitive or resistant to cisplatin. A superior biological activity of the organometallic compound clearly emerged compared to the corresponding platinum(ii) complex; the antiproliferative effects are further enhanced upon attaching the gold(i) triphenylphosphine moiety to the organometallic Pt compound. Remarkably, these novel metal species are able to overcome nearly complete resistance to cisplatin. Significant mechanistic insight into the study compounds was gained after investigating their reactions with a few representative biomolecules by electrospray mass spectrometry and X-ray crystallography. The obtained results are comprehensively discussed.

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Organizational Affiliation: 
• Department of Chemistry and Pharmacy, University of Sassari, via Vienna 2, 07100 Sassari, Italy. [e-mail].
Department of Chemistry and Pharmacy, University of Sassari, via Vienna 2, 07100 Sassari, Italy. [e-mail] and CIRCC, Consorzio Interuniversitario Reattività Chimica e Catalisi, Università di Bari, Via Celso Ulpiani 27, 70126 Bari, Italy.
Department of Health Sciences, Section of Clinical Pharmacology and Oncology, University of Florence, viale Pieraccini 6, 50139 Firenze, Italy.
Laboratory of Metals in Medicine, Department of Chemistry, University of Florence, via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy. [e-mail].
Department of Chemical Sciences, University of Naples Federico II, via Cintia, 80126, Napoli, Italy.
Department of Chemical Sciences, University of Naples Federico II, via Cintia, 80126, Napoli, Italy and CNR Institute of Biostructures and Bioimges, Via Mezzocannone 16, 80100, Napoli, Italy.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 27.77 kDa 
• Atom Count: 2,118 
• Modeled Residue Count: 248 
• Deposited Residue Count: 248 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease pancreatic	A, B	124	Bos taurus	Mutation(s): 0  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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AU	C [auth A]	GOLD ION Au ZBKIUFWVEIBQRT-UHFFFAOYSA-N
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ACT	E [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free:  0.234 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.487	α = 90
b = 31.215	β = 90.69
c = 69.012	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-12-09 
Deposition Author(s): Merlino, A.

Revision History  

• Version 1.0: 2015-12-09
  Type: Initial release
  
• Version 1.1: 2016-01-13
  Changes: Database references
• Version 2.0: 2019-10-02
  Changes: Atomic model, Data collection, Derived calculations
• Version 2.1: 2019-11-20
  Changes: Derived calculations
• Version 2.2: 2024-10-23
  Changes: Data collection, Database references, Structure summary