6T5J

Structure of NUDT15 in complex with inhibitor TH1760


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.163 

wwPDB Validation 3D Report Full Report



Literature

Development of a chemical probe against NUDT15.

Zhang, S.M.Desroses, M.Hagenkort, A.Valerie, N.C.K.Rehling, D.Carter, M.Wallner, O.Koolmeister, T.Throup, A.Jemth, A.S.Almlof, I.Loseva, O.Lundback, T.Axelsson, H.Regmi, S.Sarno, A.Kramer, A.Pudelko, L.Brautigam, L.Rasti, A.Gottmann, M.Wiita, E.Kutzner, J.Schaller, T.Kalderen, C.Cazares-Korner, A.Page, B.D.G.Krimpenfort, R.Eshtad, S.Altun, M.Rudd, S.G.Knapp, S.Scobie, M.Homan, E.J.Berglund, U.W.Stenmark, P.Helleday, T.

(2020) Nat Chem Biol 

  • DOI: 10.1038/s41589-020-0592-z
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The NUDIX hydrolase NUDT15 was originally implicated in sanitizing oxidized nucleotides, but was later shown to hydrolyze the active thiopurine metabolites, 6-thio-(d)GTP, thereby dictating the clinical response of this standard-of-care treatment for ...

    The NUDIX hydrolase NUDT15 was originally implicated in sanitizing oxidized nucleotides, but was later shown to hydrolyze the active thiopurine metabolites, 6-thio-(d)GTP, thereby dictating the clinical response of this standard-of-care treatment for leukemia and inflammatory diseases. Nonetheless, its physiological roles remain elusive. Here, we sought to develop small-molecule NUDT15 inhibitors to elucidate its biological functions and potentially to improve NUDT15-dependent chemotherapeutics. Lead compound TH1760 demonstrated low-nanomolar biochemical potency through direct and specific binding into the NUDT15 catalytic pocket and engaged cellular NUDT15 in the low-micromolar range. We also employed thiopurine potentiation as a proxy functional readout and demonstrated that TH1760 sensitized cells to 6-thioguanine through enhanced accumulation of 6-thio-(d)GTP in nucleic acids. A biochemically validated, inactive structural analog, TH7285, confirmed that increased thiopurine toxicity takes place via direct NUDT15 inhibition. In conclusion, TH1760 represents the first chemical probe for interrogating NUDT15 biology and potential therapeutic avenues.


    Organizational Affiliation

    Weston Park Cancer Centre, Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK. thomas.helleday@scilifelab.se.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Probable 8-oxo-dGTP diphosphatase NUDT15A, B164Homo sapiensMutation(s): 0 
Gene Names: NUDT15MTH2
EC: 3.6.1.9
Find proteins for Q9NV35 (Homo sapiens)
Explore Q9NV35 
Go to UniProtKB:  Q9NV35
NIH Common Fund Data Resources
PHAROS  Q9NV35
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MKB
Query on MKB

Download CCD File 
A, B
6-[4-(1~{H}-indol-5-ylcarbonyl)piperazin-1-yl]sulfonyl-3~{H}-1,3-benzoxazol-2-one
C20 H18 N4 O5 S
HNCVDRFFJZJQRW-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.163 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.79α = 90
b = 46.809β = 90
c = 137.596γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden--

Revision History 

  • Version 1.0: 2020-07-29
    Type: Initial release