8DD5

Crystal structure of KAT6A in complex with inhibitor CTx-648 (PF-9363)

• PDB DOI: https://doi.org/10.2210/pdb8DD5/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2022-06-17 Released: 2023-07-05 
• Deposition Author(s): Greasley, S.E., Johnson, E., Brodsky, O.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.58 Å
• R-Value Free: 
  0.263 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.232 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.233 (Depositor) 

Literature

Targeting KAT6A/KAT6B dependencies in breast cancer with a novel selective, orally bioavailable KAT6 inhibitor, CTx-648/PF-9363

Sharma, S., Chung, J., Uryu, S., Rickard, A., Nady, N., Cao, J., Greasley, S.E., Brodsky, O., Khan, S., Wang, H., Wang, Z., Zhang, Y., Tsaparikos, K., Chen, L., Mazurek, A., Lapek, J., Kung, P.P., Sutton, S., Richardson, P.A., Greenwald, E., Yamazaki, S., Jones, R., Maegley, K., Bingham, P., Lam, H., Stupple, A.E., Kamal, A., Chueh, A., Cuzzupe, A., Morrow, B., Ren, B., Carrasco-Pozo, C., Tan, T.W., Bhuva, D., Allan, E., Surgenor, E., Vaillant, F., Pehlivanoglu, H., Falk, H., Whittle, J., Newman, J.M., Cursons, J., Doherty, J.P., White, K.L., MacPherson, L., Devlin, M., Dennis, M.L., Hattarki, M.K., De Silva, M., Camerino, M.A., Butler, M.S., Dolezal, O., Pilling, P., Foitzik, R., Stupple, P.A., Lagiakos, R., Walker, S., Hediyeh-Zadeh, S., Nuttall, S., Spall, S., Charman, S.A., Connor, T., Peat, T.S., Avery, V.M., Bozikis, Y.E., Yang, Y., Zhang, M., Monahan, B.J., Voss, A.K., Thomas, T., Street, I.P., Dawson, S.J., Dawson, M., Lindeman, G.J., Davis, M., Visvader, J.E., Paul, T.A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: mass spectrometry

Macromolecule Content

• Total Structure Weight: 34.24 kDa 
• Atom Count: 2,286 
• Modelled Residue Count: 272 
• Deposited Residue Count: 286 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone acetyltransferase KAT6A	A	286	Homo sapiens	Mutation(s): 0  Gene Names: KAT6A, MOZ, MYST3, RUNXBP2, ZNF220 EC: 2.3.1.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q92794 (Homo sapiens) Explore Q92794  Go to UniProtKB:  Q92794
PHAROS:  Q92794 GTEx:  ENSG00000083168

Small Molecules

Ligands 2 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
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

Binding Affinity Annotations
ID	Source	Binding Affinity
R7L	BindingDB:  8DD5	Ki: min: 0.35, max: 0.83 (nM) from 8 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.58 Å
• R-Value Free:  0.263 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.232 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.233 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.63	α = 90
b = 59.63	β = 90
c = 209.89	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
PDB_EXTRACT	data extraction
autoPROC	data reduction
autoPROC	data scaling
BUSTER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-07-05 
Deposition Author(s): Greasley, S.E., Johnson, E., Brodsky, O.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-07-05
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Data collection, Structure summary