5NWH

Potent inhibitors of NUDT5 silence hormone signaling in breast cancer

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Targeted NUDT5 inhibitors block hormone signaling in breast cancer cells.

Page, B.D.G., Valerie, N.C.K., Wright, R.H.G., Wallner, O., Isaksson, R., Carter, M., Rudd, S.G., Loseva, O., Jemth, A.S., Almlof, I., Font-Mateu, J., Llona-Minguez, S., Baranczewski, P., Jeppsson, F., Homan, E., Almqvist, H., Axelsson, H., Regmi, S., Gustavsson, A.L., Lundback, T., Scobie, M., Stromberg, K., Stenmark, P., Beato, M., Helleday, T.

(2018) Nat Commun 9: 250-250

  • DOI: 10.1038/s41467-017-02293-7
  • Primary Citation of Related Structures:  
    5NWH, 5NQR

  • PubMed Abstract: 

    • With a diverse network of substrates, NUDIX hydrolases have emerged as a key family of nucleotide-metabolizing enzymes. NUDT5 (also called NUDIX5) has been implicated in ADP-ribose and 8-oxo-guanine metabolism and was recently identified as a rheosta ...

    With a diverse network of substrates, NUDIX hydrolases have emerged as a key family of nucleotide-metabolizing enzymes. NUDT5 (also called NUDIX5) has been implicated in ADP-ribose and 8-oxo-guanine metabolism and was recently identified as a rheostat of hormone-dependent gene regulation and proliferation in breast cancer cells. Here, we further elucidate the physiological relevance of known NUDT5 substrates and underscore the biological requirement for NUDT5 in gene regulation and proliferation of breast cancer cells. We confirm the involvement of NUDT5 in ADP-ribose metabolism and dissociate a relationship to oxidized nucleotide sanitation. Furthermore, we identify potent NUDT5 inhibitors, which are optimized to promote maximal NUDT5 cellular target engagement by CETSA. Lead compound, TH5427, blocks progestin-dependent, PAR-derived nuclear ATP synthesis and subsequent chromatin remodeling, gene regulation and proliferation in breast cancer cells. We herein present TH5427 as a promising, targeted inhibitor that can be used to further study NUDT5 activity and ADP-ribose metabolism.

    Organizational Affiliation: 

    Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, SE-171 21, Sweden. thomas.helleday@scilifelab.se.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ADP-sugar pyrophosphataseA, B219Homo sapiensMutation(s): 0 
Gene Names: NUDT5, NUDIX5, HSPC115
EC: 3.6.1.13 (PDB Primary Data), 3.6.1.58 (PDB Primary Data), 2.7.7.96 (PDB Primary Data)
Find proteins for Q9UKK9 (Homo sapiens)
Explore Q9UKK9 
Go to UniProtKB:  Q9UKK9
NIH Common Fund Data Resources
PHAROS  Q9UKK9
GTEx  ENSG00000165609
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9CH
Query on 9CH
Download CCD File 
A
7-[[5-(3,4-dichlorophenyl)-1,3,4-oxadiazol-2-yl]methyl]-1,3-dimethyl-8-piperazin-1-yl-purine-2,6-dione
C20 H20 Cl2 N8 O3
QXCXMVYVUHVFLP-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.191 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.561α = 90
b = 40.146β = 113.38
c = 104.064γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-04-04
    Type: Initial release
  • Version 1.1: 2019-10-16
    Changes: Data collection