5CPR

The novel SUV4-20 inhibitor A-196 verifies a role for epigenetics in genomic integrity


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

The SUV4-20 inhibitor A-196 verifies a role for epigenetics in genomic integrity.

Bromberg, K.D.Mitchell, T.R.Upadhyay, A.K.Jakob, C.G.Jhala, M.A.Comess, K.M.Lasko, L.M.Li, C.Tuzon, C.T.Dai, Y.Li, F.Eram, M.S.Nuber, A.Soni, N.B.Manaves, V.Algire, M.A.Sweis, R.F.Torrent, M.Schotta, G.Sun, C.Michaelides, M.R.Shoemaker, A.R.Arrowsmith, C.H.Brown, P.J.Santhakumar, V.Martin, A.Rice, J.C.Chiang, G.G.Vedadi, M.Barsyte-Lovejoy, D.Pappano, W.N.

(2017) Nat Chem Biol 13: 317-324

  • DOI: https://doi.org/10.1038/nchembio.2282
  • Primary Citation of Related Structures:  
    5CPR

  • PubMed Abstract: 

    Protein lysine methyltransferases (PKMTs) regulate diverse physiological processes including transcription and the maintenance of genomic integrity. Genetic studies suggest that the PKMTs SUV420H1 and SUV420H2 facilitate proficient nonhomologous end-joining (NHEJ)-directed DNA repair by catalyzing the di- and trimethylation (me2 and me3, respectively) of lysine 20 on histone 4 (H4K20). Here we report the identification of A-196, a potent and selective inhibitor of SUV420H1 and SUV420H2. Biochemical and co-crystallization analyses demonstrate that A-196 is a substrate-competitive inhibitor of both SUV4-20 enzymes. In cells, A-196 induced a global decrease in H4K20me2 and H4K20me3 and a concomitant increase in H4K20me1. A-196 inhibited 53BP1 foci formation upon ionizing radiation and reduced NHEJ-mediated DNA-break repair but did not affect homology-directed repair. These results demonstrate the role of SUV4-20 enzymatic activity in H4K20 methylation and DNA repair. A-196 represents a first-in-class chemical probe of SUV4-20 to investigate the role of histone methyltransferases in genomic integrity.


  • Organizational Affiliation

    Discovery, Research and Development, AbbVie, North Chicago, Illinois, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase SUV420H1A [auth B]268Homo sapiensMutation(s): 0 
Gene Names: SUV420H1KMT5BCGI-85
EC: 2.1.1.43
UniProt & NIH Common Fund Data Resources
Find proteins for Q4FZB7 (Homo sapiens)
Explore Q4FZB7 
Go to UniProtKB:  Q4FZB7
PHAROS:  Q4FZB7
GTEx:  ENSG00000110066 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4FZB7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SAM
Query on SAM

Download Ideal Coordinates CCD File 
C [auth B]S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
539
Query on 539

Download Ideal Coordinates CCD File 
D [auth B]6,7-dichloro-N-cyclopentyl-4-(pyridin-4-yl)phthalazin-1-amine
C18 H16 Cl2 N4
ABGOSOMRWSYAOB-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
539 Binding MOAD:  5CPR Kd: 27.8 (nM) from 1 assay(s)
BindingDB:  5CPR IC50: 25 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.209α = 90
b = 47.913β = 90
c = 129.072γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-25
    Type: Initial release
  • Version 1.1: 2017-02-08
    Changes: Database references
  • Version 1.2: 2017-02-22
    Changes: Database references
  • Version 1.3: 2023-09-27
    Changes: Data collection, Database references, Refinement description