5DNN

Nucleosome core particle containing adducts of gold(I)-triethylphosphane and ruthenium(II)-toluene PTA complexes


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.216 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Allosteric cross-talk in chromatin can mediate drug-drug synergy

Adhireksan, Z.Palermo, G.Riedel, T.Ma, Z.Muhammad, R.Rothlisberger, U.Dyson, P.J.Davey, C.A.

(2017) Nat Commun 8: 14860-14860

  • DOI: 10.1038/ncomms14860
  • Primary Citation of Related Structures:  
    5DNM, 5DNN

  • PubMed Abstract: 
  • Exploitation of drug-drug synergism and allostery could yield superior therapies by capitalizing on the immensely diverse, but highly specific, potential associated with the biological macromolecular landscape. Here we describe a drug-drug synergy mediated by allosteric cross-talk in chromatin, whereby the binding of one drug alters the activity of the second ...

    Exploitation of drug-drug synergism and allostery could yield superior therapies by capitalizing on the immensely diverse, but highly specific, potential associated with the biological macromolecular landscape. Here we describe a drug-drug synergy mediated by allosteric cross-talk in chromatin, whereby the binding of one drug alters the activity of the second. We found two unrelated drugs, RAPTA-T and auranofin, that yield a synergistic activity in killing cancer cells, which coincides with a substantially greater number of chromatin adducts formed by one of the compounds when adducts from the other agent are also present. We show that this occurs through an allosteric mechanism within the nucleosome, whereby defined histone adducts of one drug promote reaction of the other drug at a distant, specific histone site. This opens up possibilities for epigenetic targeting and suggests that allosteric modulation in nucleosomes may have biological relevance and potential for therapeutic interventions.


    Organizational Affiliation

    NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, Singapore 636921, Singapore.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3.2A, E135Xenopus laevisMutation(s): 1 
UniProt
Find proteins for P84233 (Xenopus laevis)
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UniProt GroupP84233
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4B, F102Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P62799 (Xenopus laevis)
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UniProt GroupP62799
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2AC, G128Xenopus laevisMutation(s): 0 
Gene Names: hist1h2ajLOC494591
UniProt
Find proteins for P06897 (Xenopus laevis)
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UniProt GroupP06897
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B 1.1D, H125Xenopus laevisMutation(s): 1 
UniProt
Find proteins for P02281 (Xenopus laevis)
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UniProt GroupP02281
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Entity ID: 5
MoleculeChainsLengthOrganismImage
DNA (145-MER)I 145synthetic construct
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Entity ID: 6
MoleculeChainsLengthOrganismImage
DNA (145-MER)J 145synthetic construct
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Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RAX
Query on RAX

Download Ideal Coordinates CCD File 
P [auth G],
R [auth H]
dichloro[(1,2,3,4,5,6-eta)-6-methylbenzene]1,3,5-triaza-7lambda~5~-phosphatricyclo[3.3.1.1~3,7~]dec-7-ylruthenium
C13 H20 Cl2 N3 P Ru
HQZSVEABAKKRLM-UHFFFAOYSA-M
 Ligand Interaction
AUF
Query on AUF

Download Ideal Coordinates CCD File 
K [auth A],
N [auth E]
triethylphosphanuidylgold(1+)
C6 H15 Au P
NKNLIDCIHVTIMI-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
L [auth C],
O [auth G],
Q [auth H]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG

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M [auth E]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.216 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.726α = 90
b = 109.948β = 90
c = 182.041γ = 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: 2016-09-14
    Type: Initial release
  • Version 1.1: 2017-08-16
    Changes: Database references, Derived calculations