6OIO | pdb_00006oio

Crystal structure of MYST acetyltransferase domain in complex with inhibitor 60

• PDB DOI: https://doi.org/10.2210/pdb6OIO/pdb

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


• Deposited: 2019-04-09 Released: 2019-07-03 
• Deposition Author(s): Hermans, S.J., Chung, M.C., Parker, M.W., Thomas, T., Baell, J.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.221 (Depositor), 0.218 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Literature

Discovery of Benzoylsulfonohydrazides as Potent Inhibitors of the Histone Acetyltransferase KAT6A.

Leaver, D.J., Cleary, B., Nguyen, N., Priebbenow, D.L., 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., Katneni, K., Cuellar, M., Strasser, J.M., Dahlin, J.L., Walters, M.A., Street, I.P., Monahan, B.J., Jarman, K.E., Sabroux, H.J., Falk, H., Chung, M.C., Hermans, S.J., Parker, M.W., Thomas, T., Baell, J.B.

(2019) J Med Chem 62: 7146-7159

• PubMed: 31256587 
• DOI: https://doi.org/10.1021/acs.jmedchem.9b00665
• Primary Citation Related Structures: 
  6OIN, 6OIO, 6OIP, 6OIQ, 6OIR


• PubMed Abstract: 
  

  A high-throughput screen for inhibitors of the histone acetyltransferase, KAT6A, led to identification of an aryl sulfonohydrazide derivative (CTX-0124143) that inhibited KAT6A with an IC ₅₀ of 1.0 μM. Elaboration of the structure-activity relationship and medicinal chemistry optimization led to the discovery of WM-8014 ( 97 ), a highly potent inhibitor of KAT6A (IC ₅₀ = 0.008 μM). WM-8014 competes with acetyl-CoA (Ac-CoA), and X-ray crystallographic analysis demonstrated binding to the Ac-CoA binding site. Through inhibition of KAT6A activity, WM-8014 induces cellular senescence and represents a unique pharmacological tool.

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Organizational Affiliation: 
• Cancer Therapeutics CRC , 343 Royal Parade , Parkville , Victoria 3052 , Australia.
Walter and Eliza Hall Institute of Medical Research , 1G Royal Parade , Parkville , Victoria 3052 , Australia.
Department of Medical Biology , University of Melbourne , Parkville , Victoria 3050 , Australia.
School of Pharmaceutical Sciences , Nanjing Tech University , No. 30 South Puzhu Road , Nanjing 211816 , People's Republic of China.
Institute for Therapeutics Discovery and Development , University of Minnesota , 717 Delaware Street SE , Minneapolis , Minnesota 55455 , United States.
Department of Pathology , Brigham and Women's Hospital, Boston , 75 Francis Street , Boston , Massachusetts 02115 , United States.
ACRF Rational Drug Discovery Centre , St. Vincent's Institute of Medical Research , Fitzroy , Victoria 3065 , Australia.
ARC Centre for Fragment-Based Design , Monash University , Parkville , Victoria 3052 , Australia.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 32.56 kDa 
• Atom Count: 2,443 
• Modeled Residue Count: 273 
• Deposited Residue Count: 273 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone acetyltransferase KAT8	A	273	Homo sapiens	Mutation(s): 4  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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ML7	B [auth A]	N'-(phenylsulfonyl)[1,1'-biphenyl]-3-carbohydrazide C19 H16 N2 O3 S HWMDJNJNDQETFD-UHFFFAOYSA-N
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-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: 1.70 Å
• R-Value Free:  0.221 (Depositor), 0.218 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.48	α = 90
b = 56.82	β = 90
c = 122.11	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-07-03 
Deposition Author(s): Hermans, S.J., Chung, M.C., Parker, M.W., Thomas, T., Baell, J.B.

Revision History  

• Version 1.0: 2019-07-03
  Type: Initial release
  
• Version 1.1: 2019-07-17
  Changes: Data collection, Database references
• Version 1.2: 2019-08-21
  Changes: Data collection, Database references
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary