6E2B

Ubiquitin in complex with Pt(2-phenilpyridine)(PPh3)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Reactions of Cyclometalated Platinum(II) [Pt(N∧C)(PR3)Cl] Complexes with Imidazole and Imidazole-Containing Biomolecules: Fine-Tuning of Reactivity and Photophysical Properties via Ligand Design.

Solomatina, A.I.Chelushkin, P.S.Abakumova, T.O.Zhemkov, V.A.Kim, M.Bezprozvanny, I.Gurzhiy, V.V.Melnikov, A.S.Anufrikov, Y.A.Koshevoy, I.O.Su, S.H.Chou, P.T.Tunik, S.P.

(2019) Inorg Chem 58: 204-217

  • DOI: 10.1021/acs.inorgchem.8b02204

  • PubMed Abstract: 
  • This work describes interaction of a family of [Pt(N <sup>∧ </sup>C)(PR <sub>3 </sub>)Cl] complexes with imidazole (Im), possible application of this chemistry for regioselective labeling of proteins through imidazole rings of histidine residues and ...

    This work describes interaction of a family of [Pt(N C)(PR 3 )Cl] complexes with imidazole (Im), possible application of this chemistry for regioselective labeling of proteins through imidazole rings of histidine residues and employment of the resulting phosphorescent products in bioimaging. It was found that the complexes containing aliphatic phosphines display reversible substitution of chloride ligand for imidazole function that required considerable excess of imidazole to obtain full conversion into the substituted [Pt(ppy)(PR 3 )(Im)] product, whereas the substitution in the complexes with aromatic phosphines readily proceeds in 1:1.5 mixture of reagents. Rapid, selective, and quantitative coordination of imidazole to the platinum complexes enabled regioselective labeling of ubiquitin. X-ray protein crystallography of the {[Pt(ppy)(PPh 3 )]/ubiquitin} conjugate revealed direct bonding of the platinum center to unique histidine-68 residue through the nitrogen atom of imidazole function, the coordination being also supported by noncovalent interaction of the ligands with the protein secondary structure. The variations of the cyclometalating N C ligands gave a series of [Pt(N C)(PPh 3 )Cl] complexes (N C = 2-phenylpyridine, 2-(benzofuran-3-yl)pyridine, 2-(benzo[b]thiophen-3-yl)pyridine, methyl-2-phenylquinoline-4-carboxylate), which were used to investigate the impact of N C-ligand onto photophysical properties of the imidazole complexes and conjugates with human serum albumin (HSA). The chloride ligand substitution for imidazole and formation of the conjugates results in ignition of the platinum chromophore luminescence with substantially higher quantum yield in the latter case. Variation of the metalating N C-ligand made possible the shift of the emission to the red region of visible spectrum for both types of the products. Cell-viability tests revealed low cytotoxicity of all {[Pt(N C)(PPh 3 )Cl]/HSA} conjugates, while PLIM experiments demonstrated their high potential for oxygen sensing.


    Organizational Affiliation

    Department of Chemistry , National Taiwan University , 10617 Taipei , Taiwan R.O.C.,Department of Physiology , UT Southwestern Medical Center at Dallas , 5323 Harry Hines Boulevard , Dallas 75390 , Texas , United States.,Department of Chemistry , University of Eastern Finland , 80101 Joensuu , Finland.,Center of Life Sciences , Skolkovo Institute of Science and Technology , Skolkovo, Nobel str. 3 , 143026 Moscow , Russia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin
A, C, E, G, I, P
76Bos taurusMutation(s): 0 
Gene Names: RPS27A (UBA80, UBCEP1)
Find proteins for P62992 (Bos taurus)
Go to Gene View: RPS27A
Go to UniProtKB:  P62992
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, I, P
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, C, E, I
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
PT7
Query on PT7

Download SDF File 
Download CCD File 
A, C, P
chloro[2-(pyridin-2-yl-kappaN)phenyl-kappaC~1~](triphenyl-lambda~5~-phosphanyl)platinum(2+)
PtII(2-phenylpyridine)(tri-phenylphosphine)Cl
C29 H23 Cl N P Pt
KHJLZDWNJSEPIZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.181 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 140.381α = 90.00
b = 140.381β = 90.00
c = 62.447γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data scaling
HKL-2000data reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-07-11 
  • Released Date: 2018-11-14 
  • Deposition Author(s): Zhemkov, V.A., Kim, M.

Funding OrganizationLocationGrant Number
Russian Science FoundationRussian Federation16-43-03003
Other governmentRussian Federation17.991.2017/PCh

Revision History 

  • Version 1.0: 2018-11-14
    Type: Initial release
  • Version 1.1: 2019-05-01
    Type: Data collection, Database references