8CEW | pdb_00008cew

Crystal structure of human DNA cross-link repair 1A in complex with N-hydroxyimide inhibitor H1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 
    0.224 (Depositor), 0.225 (DCC) 
  • R-Value Work: 
    0.198 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 
    0.199 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 8CEW

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

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 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.

Macromolecule Content 

  • Total Structure Weight: 39.83 kDa 
  • Atom Count: 3,027 
  • Modeled Residue Count: 341 
  • Deposited Residue Count: 345 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA cross-link repair 1A protein345Homo 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

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UFI
(Subject of Investigation/LOI)

Query on UFI



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A]
6-methoxy-2-oxidanyl-benzo[de]isoquinoline-1,3-dione
C13 H9 N O4
JNZJPCRGQNFNFC-UHFFFAOYSA-N
DMS

Query on DMS



Download:Ideal Coordinates CCD File
B [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
D [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
NI

Query on NI



Download:Ideal Coordinates CCD File
C [auth A]NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free:  0.224 (Depositor), 0.225 (DCC) 
  • R-Value Work:  0.198 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 0.199 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.59α = 90
b = 56.5β = 90
c = 113.95γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
DIALSdata 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: 2024-02-21
    Type: Initial release
  • Version 1.1: 2024-09-11
    Changes: Database references