4WU9

Structure of cisPtNAP-NCP145


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Stereochemical control of nucleosome targeting by platinum-intercalator antitumor agents.

Chua, E.Y.Davey, G.E.Chin, C.F.Droge, P.Ang, W.H.Davey, C.A.

(2015) Nucleic Acids Res 43: 5284-5296

  • DOI: 10.1093/nar/gkv356
  • Primary Citation of Related Structures:  
    4WU8, 4WU9

  • PubMed Abstract: 
  • Platinum-based anticancer drugs act therapeutically by forming DNA adducts, but suffer from severe toxicity and resistance problems, which have not been overcome in spite of decades of research. And yet defined chromatin targets have generally not been considered in the drug development process ...

    Platinum-based anticancer drugs act therapeutically by forming DNA adducts, but suffer from severe toxicity and resistance problems, which have not been overcome in spite of decades of research. And yet defined chromatin targets have generally not been considered in the drug development process. Here we designed novel platinum-intercalator species to target a highly deformed DNA site near the nucleosome center. Between two seemingly similar structural isomers, we find a striking difference in DNA site selectivity in vitro, which comes about from stereochemical constraints that limit the reactivity of the trans isomer to special DNA sequence elements while still allowing the cis isomer to efficiently form adducts at internal sites in the nucleosome core. This gives the potential for controlling nucleosome site targeting in vivo, which would engender sensitivity to epigenetic distinctions and in particular cell type/status-dependent differences in nucleosome positioning. Moreover, while both compounds yield very similar DNA-adduct structures and display antitumor cell activity rivalling that of cisplatin, the cis isomer, relative to the trans, has a much more rapid cytotoxic effect and distinct impact on cell function. The novel stereochemical principles for controlling DNA site selectivity we discovered could aid in the design of improved site discriminating agents.


    Organizational Affiliation

    School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551 davey@ntu.edu.sg.



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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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4B, F102Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P62799 (Xenopus laevis)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2A type 1C, G129Xenopus laevisMutation(s): 2 
UniProt
Find proteins for P06897 (Xenopus laevis)
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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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Go to UniProtKB:  P02281
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsLengthOrganismImage
DNA (145-MER)I145synthetic construct
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Entity ID: 6
MoleculeChainsLengthOrganismImage
DNA (145-MER)J145synthetic construct
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CX8
Query on CX8

Download Ideal Coordinates CCD File 
N [auth I], O [auth I], P [auth J][2-{3-[(2-{[2-(amino-kappaN)ethyl]amino-kappaN}ethyl)amino-kappaN]propyl}-1H-benzo[de]isoquinoline-1,3(2H)-dionato(3-)]platinum
C19 H21 N4 O2 Pt
XUMMUUAWYGZUAF-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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K [auth C], M [auth H]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
L [auth E]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.57α = 90
b = 109.33β = 90
c = 181.28γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-09-02
    Type: Initial release