6BA2

Crystal structure of MYST acetyltransferase domain in complex with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Inhibitors of histone acetyltransferases KAT6A/B induce senescence and arrest tumour growth.

Baell, J.B.Leaver, D.J.Hermans, S.J.Kelly, G.L.Brennan, M.S.Downer, N.L.Nguyen, N.Wichmann, J.McRae, H.M.Yang, Y.Cleary, B.Lagiakos, H.R.Mieruszynski, S.Pacini, G.Vanyai, H.K.Bergamasco, M.I.May, R.E.Davey, B.K.Morgan, K.J.Sealey, A.J.Wang, B.Zamudio, N.Wilcox, S.Garnham, A.L.Sheikh, B.N.Aubrey, B.J.Doggett, K.Chung, M.C.de Silva, M.Bentley, J.Pilling, P.Hattarki, M.Dolezal, O.Dennis, M.L.Falk, H.Ren, B.Charman, S.A.White, K.L.Rautela, J.Newbold, A.Hawkins, E.D.Johnstone, R.W.Huntington, N.D.Peat, T.S.Heath, J.K.Strasser, A.Parker, M.W.Smyth, G.K.Street, I.P.Monahan, B.J.Voss, A.K.Thomas, T.

(2018) Nature 560: 253-257

  • DOI: https://doi.org/10.1038/s41586-018-0387-5
  • Primary Citation of Related Structures:  
    6BA2, 6BA4, 6CT2

  • PubMed Abstract: 

    Acetylation of histones by lysine acetyltransferases (KATs) is essential for chromatin organization and function 1 . Among the genes coding for the MYST family of KATs (KAT5-KAT8) are the oncogenes KAT6A (also known as MOZ) and KAT6B (also known as MORF and QKF) 2,3 . KAT6A has essential roles in normal haematopoietic stem cells 4-6 and is the target of recurrent chromosomal translocations, causing acute myeloid leukaemia 7,8 . Similarly, chromosomal translocations in KAT6B have been identified in diverse cancers 8 . KAT6A suppresses cellular senescence through the regulation of suppressors of the CDKN2A locus 9,10 , a function that requires its KAT activity 10 . Loss of one allele of KAT6A extends the median survival of mice with MYC-induced lymphoma from 105 to 413 days 11 . These findings suggest that inhibition of KAT6A and KAT6B may provide a therapeutic benefit in cancer. Here we present highly potent, selective inhibitors of KAT6A and KAT6B, denoted WM-8014 and WM-1119. Biochemical and structural studies demonstrate that these compounds are reversible competitors of acetyl coenzyme A and inhibit MYST-catalysed histone acetylation. WM-8014 and WM-1119 induce cell cycle exit and cellular senescence without causing DNA damage. Senescence is INK4A/ARF-dependent and is accompanied by changes in gene expression that are typical of loss of KAT6A function. WM-8014 potentiates oncogene-induced senescence in vitro and in a zebrafish model of hepatocellular carcinoma. WM-1119, which has increased bioavailability, arrests the progression of lymphoma in mice. We anticipate that this class of inhibitors will help to accelerate the development of therapeutics that target gene transcription regulated by histone acetylation.


  • Organizational Affiliation

    Medicinal Chemistry Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia. Jonathan.Baell@monash.edu.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone acetyltransferase KAT8295Homo sapiensMutation(s): 0 
Gene Names: KAT8MOFMYST1PP7073
EC: 2.3.1.48 (PDB Primary Data), 2.3.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H7Z6 (Homo sapiens)
Explore Q9H7Z6 
Go to UniProtKB:  Q9H7Z6
PHAROS:  Q9H7Z6
GTEx:  ENSG00000103510 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H7Z6
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
7KM (Subject of Investigation/LOI)
Query on 7KM

Download Ideal Coordinates CCD File 
J [auth A]4-fluoro-5-methyl-N'-(phenylsulfonyl)[1,1'-biphenyl]-3-carbohydrazide
C20 H17 F N2 O3 S
PHHZKBMVRPULAW-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A],
G [auth A],
I [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
B [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
H [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
ALY
Query on ALY
A
L-PEPTIDE LINKINGC8 H16 N2 O3LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.231α = 90
b = 56.916β = 90
c = 120.999γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia1030704
National Health and Medical Research Council (NHMRC, Australia)Australia1080146

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-01
    Type: Initial release
  • Version 1.1: 2018-08-15
    Changes: Data collection, Database references
  • Version 1.2: 2018-08-22
    Changes: Data collection, Database references
  • Version 1.3: 2020-01-08
    Changes: Author supporting evidence
  • Version 1.4: 2024-10-23
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary