7OTY

DNA-PKcs in complex with M3814


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.96 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Structural insights into inhibitor regulation of the DNA repair protein DNA-PKcs.

Liang, S.Thomas, S.E.Chaplin, A.K.Hardwick, S.W.Chirgadze, D.Y.Blundell, T.L.

(2022) Nature 601: 643-648

  • DOI: https://doi.org/10.1038/s41586-021-04274-9
  • Primary Citation of Related Structures:  
    7OTM, 7OTP, 7OTV, 7OTW, 7OTY

  • PubMed Abstract: 

    The DNA-dependent protein kinase catalytic subunit (DNA-PKcs) has a central role in non-homologous end joining, one of the two main pathways that detect and repair DNA double-strand breaks (DSBs) in humans 1,2 . DNA-PKcs is of great importance in repairing pathological DSBs, making DNA-PKcs inhibitors attractive therapeutic agents for cancer in combination with DSB-inducing radiotherapy and chemotherapy 3 . Many of the selective inhibitors of DNA-PKcs that have been developed exhibit potential as treatment for various cancers 4 . Here we report cryo-electron microscopy (cryo-EM) structures of human DNA-PKcs natively purified from HeLa cell nuclear extracts, in complex with adenosine-5'-(γ-thio)-triphosphate (ATPγS) and four inhibitors (wortmannin, NU7441, AZD7648 and M3814), including drug candidates undergoing clinical trials. The structures reveal molecular details of ATP binding at the active site before catalysis and provide insights into the modes of action and specificities of the competitive inhibitors. Of note, binding of the ligands causes movement of the PIKK regulatory domain (PRD), revealing a connection between the p-loop and PRD conformations. Electrophoretic mobility shift assay and cryo-EM studies on the DNA-dependent protein kinase holoenzyme further show that ligand binding does not have a negative allosteric or inhibitory effect on assembly of the holoenzyme complex and that inhibitors function through direct competition with ATP. Overall, the structures described in this study should greatly assist future efforts in rational drug design targeting DNA-PKcs, demonstrating the potential of cryo-EM in structure-guided drug development for large and challenging targets.


  • Organizational Affiliation

    Department of Biochemistry, University of Cambridge, Cambridge, UK. sl744@cam.ac.uk.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-dependent protein kinase catalytic subunit,DNA-PKcs4,148Homo sapiensMutation(s): 0 
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P78527 (Homo sapiens)
Explore P78527 
Go to UniProtKB:  P78527
PHAROS:  P78527
GTEx:  ENSG00000253729 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP78527
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1IX (Subject of Investigation/LOI)
Query on 1IX

Download Ideal Coordinates CCD File 
B [auth A](~{S})-[2-chloranyl-4-fluoranyl-5-(7-morpholin-4-ylquinazolin-4-yl)phenyl]-(6-methoxypyridazin-3-yl)methanol
C24 H21 Cl F N5 O3
MOWXJLUYGFNTAL-DEOSSOPVSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
1IX BindingDB:  7OTY IC50: min: 3, max: 19 (nM) from 4 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.96 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-12
    Type: Initial release
  • Version 1.1: 2022-01-19
    Changes: Database references
  • Version 1.2: 2022-02-02
    Changes: Structure summary
  • Version 1.3: 2022-02-09
    Changes: Database references
  • Version 1.4: 2022-10-05
    Changes: Structure summary
  • Version 1.5: 2024-07-17
    Changes: Data collection