9S1N | pdb_00009s1n

Crystal structure of DNPH1 bound by compound 19


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.229 (Depositor), 0.225 (DCC) 
  • R-Value Work: 
    0.210 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 
    0.210 (Depositor) 

Starting Model: experimental
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Literature

Discovery and Characterization of Diverse Non-nucleotide Inhibitors of DNPH1 Using an Integrated Hit Finding Strategy.

Whitehurst, B.C.Anderson, N.A.Argyrou, A.Astles, P.Barlaam, B.Cadogan, E.B.Carlino, L.Collie, G.W.Edwards, A.Kitching, L.Li, Y.Milbradt, A.G.Nikkila, J.Northall, S.Pahlen, S.Patel, S.Savory, W.Schade, M.Spencer, J.A.Stead, D.Stubbs, C.J.Wang, A.Wang, W.

(2026) ACS Med Chem Lett 17: 226-234

  • DOI: https://doi.org/10.1021/acsmedchemlett.5c00651
  • Primary Citation of Related Structures:  
    9RPO, 9S0O, 9S1N, 9S1O

  • PubMed Abstract: 

    DNPH1 is a hydrolase enzyme that degrades the noncanonical nucleotide 5-hydroxymethyl-2'-deoxyuridine 5'-monophosphate (hmdUMP), thus acting as a nucleotide pool sanitizer by preventing its aberrant incorporation into DNA. Recent studies have shown that loss of DNPH1 enhances the sensitivity of homologous recombination repair-deficient cancer cells to PARP inhibitors, highlighting its potential as an attractive therapeutic target. Herein we report the design and prosecution of an integrated hit finding strategy combining high-throughput screening, DNA-encoded library screening, and fragment-based lead generation which enabled the discovery of the first non-nucleotide ligands for DNPH1. We compare four hit compounds which differ markedly in their chemical structures, physicochemical properties, and binding modes and summarize parallel hit-to-lead workup efforts. We also provide discussion of the merits of an integrated approach for hit discovery when applied to challenging novel targets such as DNPH1.


  • Organizational Affiliation
    • Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, United Kingdom.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
5-hydroxymethyl-dUMP N-hydrolase152Homo sapiensMutation(s): 0 
Gene Names: DNPH1C6orf108RCL
EC: 3.2.2
UniProt & NIH Common Fund Data Resources
Find proteins for O43598 (Homo sapiens)
Explore O43598 
Go to UniProtKB:  O43598
PHAROS:  O43598
GTEx:  ENSG00000112667 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO43598
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1JKZ (Subject of Investigation/LOI)
Query on A1JKZ

Download Ideal Coordinates CCD File 
B [auth A]2-[[3-(7-bromanyl-1,2,4,5-tetrahydro-3-benzazepin-3-yl)-1,2,4-oxadiazol-5-yl]methyl]-3,4-dihydro-1~{H}-isoquinoline-7-carboxylic acid
C23 H23 Br N4 O3
LMIHZOOKIJYEAW-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.229 (Depositor), 0.225 (DCC) 
  • R-Value Work:  0.210 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 0.210 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.026α = 90
b = 84.522β = 90
c = 33.839γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2025-12-24 
  • Deposition Author(s): Collie, G.W.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-24
    Type: Initial release
  • Version 1.1: 2026-01-28
    Changes: Database references