4XUJ | pdb_00004xuj

Nucleosome core particle containing adducts from treatment with a thiomorpholine-substituted [(eta-6-p-cymene)Ru(3-hydroxy-2-pyridone)Cl] compound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.18 Å
  • R-Value Free: 
    0.299 (Depositor), 0.290 (DCC) 
  • R-Value Work: 
    0.263 (Depositor), 0.252 (DCC) 
  • R-Value Observed: 
    0.265 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Functionalization of Ruthenium(II)( eta 6 -p-cymene)(3-hydroxy-2-pyridone) Complexes with (Thio)Morpholine: Synthesis and Bioanalytical Studies.

Hanif, M.Meier, S.M.Adhireksan, Z.Henke, H.Martic, S.Movassaghi, S.Labib, M.Kandioller, W.Jamieson, S.M.F.Hejl, M.Jakupec, M.A.Kraatz, H.B.Davey, C.A.Keppler, B.K.Hartinger, C.G.

(2017) Chempluschem 82: 841-847

  • DOI: https://doi.org/10.1002/cplu.201700050
  • Primary Citation Related Structures: 
    4XUJ

  • PubMed Abstract: 

    Hydroxypyr(id)ones constitute an emerging platform for the design of drug molecules, owing to their favorable biocompatibility and toxicity profiles. Herein, [Ru II 6 -p-cymene)] complexes with 3-hydroxy-2-pyridinone functionalized with morpholine and thiomorpholine, as a means often used in medicinal chemistry to alter the physicochemical properties of drug compounds, are reported. The compounds underwent hydrolysis of the Ru-Cl bond and the aqua species were stable for up to 48 h in aqueous solution, as observed by 1 H NMR spectroscopy and ESI-MS. The compounds formed adducts with amino acids and proteins through cleavage of the pyridinone ligand. Binding experiments to the nucleosome core particle by means of X-ray crystallography revealed similar reactivity and exclusive binding to histidine moieties of the histone proteins. Preliminary cyclin-dependent kinase 2 (CDK2)/cyclin A kinase inhibitory studies revealed promising activity similar to that of structurally related organometallic compounds.


  • Organizational Affiliation
    • School of Chemical Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand.

Macromolecule Content 

  • Total Structure Weight: 199.15 kDa 
  • Atom Count: 12,075 
  • Modeled Residue Count: 1,055 
  • Deposited Residue Count: 1,270 
  • Unique protein chains: 4
  • Unique nucleic acid chains: 2

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H3.2
A, E
135Xenopus laevisMutation(s): 1 
UniProt
Find proteins for P84233 (Xenopus laevis)
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Go to UniProtKB:  P84233
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UniProt GroupP84233
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H4
B, F
102Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P62799 (Xenopus laevis)
Explore P62799 
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UniProt GroupP62799
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H2A
C, G
128Xenopus laevisMutation(s): 0 
Gene Names: hist1h2ajLOC494591
UniProt
Find proteins for P06897 (Xenopus laevis)
Explore P06897 
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UniProt GroupP06897
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H2B 1.1
D, H
125Xenopus laevisMutation(s): 1 
UniProt
Find proteins for P02281 (Xenopus laevis)
Explore P02281 
Go to UniProtKB:  P02281
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UniProt GroupP02281
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Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (145-MER)145synthetic construct
Sequence Annotations
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Reference Sequence
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (145-MER)145synthetic construct
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
4A6

Query on 4A6



Download:Ideal Coordinates CCD File
L [auth D],
P [auth H],
Q [auth H]
[(1,2,3,4,5,6-eta)-1-methyl-4-(propan-2-yl)benzene]ruthenium
C10 H14 Ru
UGCPEEMQJJGXOS-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
K [auth C],
N [auth G],
O [auth H]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
MG

Query on MG



Download:Ideal Coordinates CCD File
M [auth E]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.18 Å
  • R-Value Free:  0.299 (Depositor), 0.290 (DCC) 
  • R-Value Work:  0.263 (Depositor), 0.252 (DCC) 
  • R-Value Observed: 0.265 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.426α = 90
b = 109.754β = 90
c = 181.277γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-01-27
    Type: Initial release
  • Version 1.1: 2016-03-02
    Changes: Structure summary
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2025-08-20
    Changes: Database references, Structure summary