9OO9 | pdb_00009oo9

Crystal structure of MYST acetyltransferase domain in complex with inhibitor 6

• PDB DOI: https://doi.org/10.2210/pdb9OO9/pdb

• Classification: TRANSFERASE/INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2025-05-15 Released: 2026-02-11 
• Deposition Author(s): Hermans, S.J., Suwandi, A., Parker, M.W., Baell, J.B.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.238 (Depositor), 0.237 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

Biological Activity and Structural Biology of Current KAT6A Inhibitor Chemotypes.

Suwandi, A., Jin, J., Zhao, Y., Mudududdla, R., Gee, Y.S., Deora, G.S., Sun, Y., Wei, H., Huang, F., He, J.S., George, A.J., Hermans, S.J., Leaver, D.J., Parker, M.W., Baell, J.B.

(2026) J Med Chem 

• PubMed: 41611522 
• DOI: https://doi.org/10.1021/acs.jmedchem.5c01426
• Primary Citation of Related Structures:  
  9OO9, 9OOA, 9OOB, 9OOC, 9OOD, 9OOE, 9OOF, 9OOH, 9OOJ


• PubMed Abstract: 
  

  All lysine acetyltransferases (KATs) modulate biological outcomes through the acetylation of lysine side-chain amino groups facilitated by acetyl coenzyme A (AcCoA). KAT6A belongs to the class of MYST domain histone acetyltransferases (HATs), which had been regarded as undruggable. The first on-target KAT6A inhibitors with in vivo activity were reported in 2018, catalyzing intense industry interest in this enzyme as an oncology target. In this study, we experimentally evaluated representative KAT6A inhibitor chemotypes through resynthesis and comparative biochemical assays, cellular assays, and structural biology. We outline the recent history of each KAT6A inhibitor chemotype discovery, including SAR for potency, selectivity, and cellular activity. We extensively benchmark key compounds from each chemotype, augmented by new acylsulfonohydrazide analogues and a novel fused [1,2,4]thiadiazine KAT6A inhibitor subclass, which we report here for the first time, along with co-crystal structures. Additionally, we report on the in vivo activity, pharmacokinetics, and toxicology profiles of these inhibitors.

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Organizational Affiliation: 
• Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville Campus), Parkville, VIC 3052, Australia.
Institute for Advanced and Applied Chemical Synthesis, College of Pharmacy, Jinan University, Guangzhou, Guangdong 510632, China.
School of Pharmaceutical Sciences, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China.
John Curtin School of Medical Research, Australian National University, Canberra, ACT 2600, Australia.
ACRF Rational Drug Discovery Centre, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia.
Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, VIC 3010, Australia.
School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia.
Australian Translational Medicinal Chemistry Facility (ATMCF), Monash University, Parkville, VIC 3052, Australia.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 35.22 kDa 
• Atom Count: 2,515 
• Modeled Residue Count: 265 
• Deposited Residue Count: 295 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone acetyltransferase KAT8	A	295	Homo sapiens	Mutation(s): 5  Gene Names: KAT8, MOF, MYST1, PP7073 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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
R7L (Subject of Investigation/LOI)	B [auth A]	2,6-dimethoxy-N-{4-methoxy-6-[(1H-pyrazol-1-yl)methyl]-1,2-benzoxazol-3-yl}benzene-1-sulfonamide C20 H20 N4 O6 S VNSQFPFWUAZOTQ-UHFFFAOYSA-N
GOL	H [auth A], I [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
NA	D [auth A], E [auth A], F [auth A], G [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ALY	A	L-PEPTIDE LINKING	C8 H16 N2 O3		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.238 (Depositor), 0.237 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.497	α = 90
b = 58.035	β = 90
c = 121.014	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrysalisPro	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2026-02-11 
Deposition Author(s): Hermans, S.J., Suwandi, A., Parker, M.W., Baell, J.B.

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Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	1030704
National Health and Medical Research Council (NHMRC, Australia)	Australia	1080146
National Health and Medical Research Council (NHMRC, Australia)	Australia	1117602
National Health and Medical Research Council (NHMRC, Australia)	Australia	APP1194263

Revision History  

• Version 1.0: 2026-02-11
  Type: Initial release