6PD8

Crystal structure of MYST acetyltransferase domain in complex with inhibitor 39


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.74 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Discovery of Acylsulfonohydrazide-Derived Inhibitors of the Lysine Acetyltransferase, KAT6A, as Potent Senescence-Inducing Anti-Cancer Agents.

Priebbenow, D.L.Leaver, D.J.Nguyen, N.Cleary, B.Lagiakos, H.R.Sanchez, J.Xue, L.Huang, F.Sun, Y.Mujumdar, P.Mudududdla, R.Varghese, S.Teguh, S.Charman, S.A.White, K.L.Shackleford, D.M.Katneni, K.Cuellar, M.Strasser, J.M.Dahlin, J.L.Walters, M.A.Street, I.P.Monahan, B.J.Jarman, K.E.Jousset Sabroux, H.Falk, H.Chung, M.C.Hermans, S.J.Downer, N.L.Parker, M.W.Voss, A.K.Thomas, T.Baell, J.B.

(2020) J Med Chem 63: 4655-4684

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b02071
  • Primary Citation of Related Structures:  
    6OWH, 6OWI, 6PD8, 6PD9, 6PDA, 6PDB, 6PDC, 6PDD, 6PDE, 6PDF, 6PDG

  • PubMed Abstract: 

    A high-throughput screen designed to discover new inhibitors of histone acetyltransferase KAT6A uncovered CTX-0124143 ( 1 ), a unique aryl acylsulfonohydrazide with an IC 50 of 1.0 μM. Using this acylsulfonohydrazide as a template, we herein disclose the results of our extensive structure-activity relationship investigations, which resulted in the discovery of advanced compounds such as 55 and 80 . These two compounds represent significant improvements on our recently reported prototypical lead WM-8014 ( 3 ) as they are not only equivalently potent as inhibitors of KAT6A but are less lipophilic and significantly more stable to microsomal degradation. Furthermore, during this process, we discovered a distinct structural subclass that contains key 2-fluorobenzenesulfonyl and phenylpyridine motifs, culminating in the discovery of WM-1119 ( 4 ). This compound is a highly potent KAT6A inhibitor (IC 50 = 6.3 nM; K D = 0.002 μM), competes with Ac-CoA by binding to the Ac-CoA binding site, and has an oral bioavailability of 56% in rats.


  • Organizational Affiliation

    Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville Campus), Parkville, Victoria 3052, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone acetyltransferase KAT8272Homo sapiensMutation(s): 5 
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 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
O9D (Subject of Investigation/LOI)
Query on O9D

Download Ideal Coordinates CCD File 
F [auth A]5-ethoxy-2-fluoro-3-methyl-N'-(phenylsulfonyl)benzohydrazide
C16 H17 F N2 O4 S
JKKRGQGRKITOSW-UHFFFAOYSA-N
GOL
Query on GOL

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

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

Download Ideal Coordinates CCD File 
C [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: 2.74 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.067α = 90
b = 56.656β = 90
c = 123.041γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-01
    Type: Initial release
  • Version 1.1: 2020-05-27
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2023-11-15
    Changes: Data collection
  • Version 1.4: 2024-10-23
    Changes: Structure summary