8C8S

Crystal structure of human DNA cross-link repair 1A in complex with hydroxamic acid inhibitor (compound 21).


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Cell-active small molecule inhibitors validate the SNM1A DNA repair nuclease as a cancer target.

Bielinski, M.Henderson, L.R.Yosaatmadja, Y.Swift, L.P.Baddock, H.T.Bowen, M.J.Brem, J.Jones, P.S.McElroy, S.P.Morrison, A.Speake, M.van Boeckel, S.van Doornmalen, E.van Groningen, J.van den Hurk, H.Gileadi, O.Newman, J.A.McHugh, P.J.Schofield, C.J.

(2024) Chem Sci 15: 8227-8241

  • DOI: https://doi.org/10.1039/d4sc00367e
  • Primary Citation of Related Structures:  
    8C8B, 8C8D, 8C8S, 8CEW, 8CF0, 8CG9

  • PubMed Abstract: 

    The three human SNM1 metallo-β-lactamase fold nucleases (SNM1A-C) play key roles in DNA damage repair and in maintaining telomere integrity. Genetic studies indicate that they are attractive targets for cancer treatment and to potentiate chemo- and radiation-therapy. A high-throughput screen for SNM1A inhibitors identified diverse pharmacophores, some of which were shown by crystallography to coordinate to the di-metal ion centre at the SNM1A active site. Structure and turnover assay-guided optimization enabled the identification of potent quinazoline-hydroxamic acid containing inhibitors, which bind in a manner where the hydroxamic acid displaces the hydrolytic water and the quinazoline ring occupies a substrate nucleobase binding site. Cellular assays reveal that SNM1A inhibitors cause sensitisation to, and defects in the resolution of, cisplatin-induced DNA damage, validating the tractability of MBL fold nucleases as cancer drug targets.


  • Organizational Affiliation

    Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford Mansfield Road Oxford OX1 3TA UK christopher.schofield@chem.ox.ac.uk.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA cross-link repair 1A protein343Homo sapiensMutation(s): 0 
Gene Names: DCLRE1AKIAA0086SNM1SNM1A
EC: 3.5.2.6
UniProt & NIH Common Fund Data Resources
Find proteins for Q6PJP8 (Homo sapiens)
Explore Q6PJP8 
Go to UniProtKB:  Q6PJP8
PHAROS:  Q6PJP8
GTEx:  ENSG00000198924 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6PJP8
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.684α = 90
b = 57.321β = 90
c = 113.73γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cancer Research UKUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-31
    Type: Initial release
  • Version 1.1: 2024-09-11
    Changes: Database references