8OTV

Crystal structure of NUDT14 complexed with novel compound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.207 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Unexpected Noncovalent Off-Target Activity of Clinical BTK Inhibitors Leads to Discovery of a Dual NUDT5/14 Antagonist.

Balikci, E.Marques, A.M.C.Bauer, L.G.Seupel, R.Bennett, J.Raux, B.Buchan, K.Simelis, K.Singh, U.Rogers, C.Ward, J.Cheng, C.Szommer, T.Schutzenhofer, K.Elkins, J.M.Sloman, D.L.Ahel, I.Fedorov, O.Brennan, P.E.Huber, K.V.M.

(2024) J Med Chem 67: 7245-7259

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c00072
  • Primary Citation of Related Structures:  
    8OTV, 8RDZ, 8RIY

  • PubMed Abstract: 

    Cofactor mimicry represents an attractive strategy for the development of enzyme inhibitors but can lead to off-target effects due to the evolutionary conservation of binding sites across the proteome. Here, we uncover the ADP-ribose (ADPr) hydrolase NUDT5 as an unexpected, noncovalent, off-target of clinical BTK inhibitors. Using a combination of biochemical, biophysical, and intact cell NanoBRET assays as well as X-ray crystallography, we confirm catalytic inhibition and cellular target engagement of NUDT5 and reveal an unusual binding mode that is independent of the reactive acrylamide warhead. Further investigation of the prototypical BTK inhibitor ibrutinib also revealed potent inhibition of the largely unstudied NUDIX hydrolase family member NUDT14. By exploring structure-activity relationships (SARs) around the core scaffold, we identify a potent, noncovalent, and cell-active dual NUDT5/14 inhibitor. Cocrystallization experiments yielded new insights into the NUDT14 hydrolase active site architecture and inhibitor binding, thus providing a basis for future chemical probe design.


  • Organizational Affiliation

    Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uridine diphosphate glucose pyrophosphatase NUDT14
A, B
223Homo sapiensMutation(s): 0 
Gene Names: NUDT14UGPP
EC: 3.6.1.45
UniProt & NIH Common Fund Data Resources
Find proteins for O95848 (Homo sapiens)
Explore O95848 
Go to UniProtKB:  O95848
PHAROS:  O95848
GTEx:  ENSG00000183828 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO95848
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.207 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.25α = 90
b = 90.967β = 90
c = 108.099γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
Aimlessdata scaling
Aimlessphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Innovative Medicines InitiativeSwitzerland875510

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-01
    Type: Initial release
  • Version 1.1: 2024-05-22
    Changes: Database references