8BOV | pdb_00008bov

X-ray structure of the adduct formed upon reaction of the five-coordinate Pt(II) complex, 1-Me,Me, with HEWL at pH 7.5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 
    0.218 (Depositor), 0.242 (DCC) 
  • R-Value Work: 
    0.182 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Impact of Hydrophobic Chains in Five-Coordinate Glucoconjugate Pt(II) Anticancer Agents.

Annunziata, A.Imbimbo, P.Cucciolito, M.E.Ferraro, G.Langellotti, V.Marano, A.Melchiorre, M.Tito, G.Trifuoggi, M.Monti, D.M.Merlino, A.Ruffo, F.

(2023) Int J Mol Sci 24

  • DOI: https://doi.org/10.3390/ijms24032369
  • Primary Citation Related Structures: 
    8BOV, 8BOY

  • PubMed Abstract: 

    This study describes new platinum(II) cationic five-coordinate complexes ( 1-R,R' ) of the formula [PtR(NHC)(dmphen)(ethene)]CF 3 SO 3 (dmphen = 2,9-dimethyl-1,10-phenanthroline), containing in their axial positions an alkyl group R (methyl or octyl) and an imidazole-based NHC-carbene ligand with a substituent R' of variable length (methyl or octyl) on one nitrogen atom. The Pt-carbene bond is stable both in DMSO and in aqueous solvents. In DMSO, a gradual substitution of dmphen and ethene is observed, with the formation of a square planar solvated species. Octanol/water partitioning studies have revealed the order of hydrophobicity of the complexes ( 1-Oct,Me > 1-Oct,Oct > 1-Me,Oct > 1-Me,Me ). Their biological activity was investigated against two pairs of cancer and non-cancer cell lines. The tested drugs were internalized in cancer cells and able to activate the apoptotic pathway. The reactivity of 1-Me,Me with DNA and protein model systems was also studied using UV-vis absorption spectroscopy, fluorescence, and X-ray crystallography. The compound binds DNA and interacts in various ways with the model protein lysozyme. Remarkably, structural data revealed that the complex can bind lysozyme via non-covalent interactions, retaining its five-coordinate geometry.


  • Organizational Affiliation
    • Institute Parisien de Chimie Moléculaire, Campus Pierre et Marie Curie, Sorbonne Université, 4 Place Jussieu, 75005 Paris, France.

Macromolecule Content 

  • Total Structure Weight: 15.37 kDa 
  • Atom Count: 1,254 
  • Modeled Residue Count: 129 
  • Deposited Residue Count: 129 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
LysozymeA [auth AAA]129Gallus 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
R0I
(Subject of Investigation/LOI)

Query on R0I



Download:Ideal Coordinates CCD File
E [auth AAA]1-[1,3-dimethyl-4-(1~{H}-1,2,3-triazol-5-yl)imidazol-1-ium-2-yl]-1,2',11'-trimethyl-spiro[1$l^{6}-platinacycloprop-2-ene-1,15'-1,12-diaza-15$l^{6}-platinatetracyclo[10.2.1.0^{5,14}.0^{8,13}]pentadeca-2,4,6,8,10,13-hexaene]
C24 H26 N7 Pt
DGCRSFURYLTMIA-UHFFFAOYSA-N
EPE

Query on EPE



Download:Ideal Coordinates CCD File
B [auth AAA]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
DMS

Query on DMS



Download:Ideal Coordinates CCD File
F [auth AAA]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
C [auth AAA],
D [auth AAA]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free:  0.218 (Depositor), 0.242 (DCC) 
  • R-Value Work:  0.182 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.58α = 90
b = 78.58β = 90
c = 37.05γ = 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: 2023-02-22
    Type: Initial release
  • Version 1.1: 2024-02-07
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-11-06
    Changes: Structure summary