7B66

Structure of NUDT15 R139H Mutant in complex with TH7755


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.185 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Literature

Crystal structures of NUDT15 variants enabled by a potent inhibitor reveal the structural basis for thiopurine sensitivity.

Rehling, D.Zhang, S.M.Jemth, A.S.Koolmeister, T.Throup, A.Wallner, O.Scaletti, E.Moriyama, T.Nishii, R.Davies, J.Desroses, M.Rudd, S.G.Scobie, M.Homan, E.Berglund, U.W.Yang, J.J.Helleday, T.Stenmark, P.

(2021) J Biol Chem 296: 100568-100568

  • DOI: https://doi.org/10.1016/j.jbc.2021.100568
  • Primary Citation of Related Structures:  
    7B63, 7B64, 7B65, 7B66, 7B67

  • PubMed Abstract: 

    The enzyme NUDT15 efficiently hydrolyzes the active metabolites of thiopurine drugs, which are routinely used for treating cancer and inflammatory diseases. Loss-of-function variants in NUDT15 are strongly associated with thiopurine intolerance, such as leukopenia, and preemptive NUDT15 genotyping has been clinically implemented to personalize thiopurine dosing. However, understanding the molecular consequences of these variants has been difficult, as no structural information was available for NUDT15 proteins encoded by clinically actionable pharmacogenetic variants because of their inherent instability. Recently, the small molecule NUDT15 inhibitor TH1760 has been shown to sensitize cells to thiopurines, through enhanced accumulation of 6-thio-guanine in DNA. Building upon this, we herein report the development of the potent and specific NUDT15 inhibitor, TH7755. TH7755 demonstrates a greatly improved cellular target engagement and 6-thioguanine potentiation compared with TH1760, while showing no cytotoxicity on its own. This potent inhibitor also stabilized NUDT15, enabling analysis by X-ray crystallography. We have determined high-resolution structures of the clinically relevant NUDT15 variants Arg139Cys, Arg139His, Val18Ile, and V18_V19insGlyVal. These structures provide clear insights into the structural basis for the thiopurine intolerance phenotype observed in patients carrying these pharmacogenetic variants. These findings will aid in predicting the effects of new NUDT15 sequence variations yet to be discovered in the clinic.


  • Organizational Affiliation

    Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleotide triphosphate diphosphatase NUDT15
A, B, C, D
164Homo sapiensMutation(s): 1 
Gene Names: NUDT15MTH2
EC: 3.6.1.9
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NV35 (Homo sapiens)
Explore Q9NV35 
Go to UniProtKB:  Q9NV35
PHAROS:  Q9NV35
GTEx:  ENSG00000136159 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NV35
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.185 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.276α = 100.08
b = 60.215β = 104.102
c = 69.303γ = 90.25
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden2018-03406

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-24
    Type: Initial release
  • Version 1.1: 2021-03-31
    Changes: Database references
  • Version 1.2: 2021-04-07
    Changes: Database references
  • Version 1.3: 2021-07-21
    Changes: Database references
  • Version 1.4: 2024-01-31
    Changes: Data collection, Database references, Derived calculations, Refinement description