9BIG | pdb_00009big

Stat6 bound to degrader AK-1690

• PDB DOI: https://doi.org/10.2210/pdb9BIG/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-04-23 Released: 2024-10-02 
• Deposition Author(s): Mallik, L., Stuckey, J.A.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 
  0.289 (Depositor), 0.298 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: experimental

Literature

Discovery of AK-1690: A Potent and Highly Selective STAT6 PROTAC Degrader.

Kaneshige, A., Yang, Y., Bai, L., Wang, M., Xu, R., Mallik, L., Chinnaswamy, K., Metwally, H., Wang, Y., McEachern, D., Tosovic, J., Yang, C.Y., Kirchhoff, P.D., Meagher, J.L., Stuckey, J.A., Wang, S.

(2025) J Med Chem 68: 5125-5151

• PubMed: 39311434 
• DOI: https://doi.org/10.1021/acs.jmedchem.4c01009
• Primary Citation Related Structures: 
  9BIG


• PubMed Abstract: 
  

  STAT6 is an attractive therapeutic target for human cancers and other human diseases. Starting from a STAT6 ligand with K _i = 3.5 μM binding affinity, we obtained AK-068 with K _i = 6 nM to STAT6 and at least >85-fold binding selectivity over STAT5. Using AK-068 and cereblon ligands, we discovered AK-1690 as the first, potent and selective PROTAC STAT6 degrader. AK-1690 effectively induces degradation of STAT6 protein in cells with DC ₅₀ values of as low as 1 nM while showing minimal effect on other STAT members up to 10 μM. A single dose of AK-1690 effectively depletes STAT6 in mouse tissues. Determination of the first cocrystal structure of STAT6 in complex with AK-1690 provides a structural basis for their interactions. AK-1690 is a powerful tool with which to investigate the roles of STAT6 in human diseases and biological processes and a promising lead compound for further optimization.

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Organizational Affiliation: 
• Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States.
Department of Internal Medicine, Medical School, University of Michigan, Ann Arbor, Michigan 48109, United States.
Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States.
Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States.
Department of Pharmacology, Medical School, University of Michigan, Ann Arbor, Michigan 48109, United States.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 62.24 kDa 
• Atom Count: 3,423 
• Modeled Residue Count: 409 
• Deposited Residue Count: 546 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Signal transducer and activator of transcription 6	A	546	Homo sapiens	Mutation(s): 0  Gene Names: STAT6
UniProt & NIH Common Fund Data Resources
Find proteins for P42226 (Homo sapiens) Explore P42226  Go to UniProtKB:  P42226
PHAROS:  P42226 GTEx:  ENSG00000166888

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1AQQ (Subject of Investigation/LOI)	B [auth A]	[(2-{[(2S)-1-{(2S,4S)-4-[(7-{2-[(3R)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-4-yl}hept-6-yn-1-yl)oxy]-2-[(2R)-2-phenylmorpholine-4-carbonyl]pyrrolidin-1-yl}-3,3-dimethyl-1-oxobutan-2-yl]carbamoyl}-1-benzothiophen-5-yl)di(fluoro)methyl]phosphonic acid C51 H56 F2 N5 O11 P S BOMRVPKXCINUMI-ZEGZQYLTSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free:  0.289 (Depositor), 0.298 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.505	α = 90
b = 103.505	β = 90
c = 53.059	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-10-02 
Deposition Author(s): Mallik, L., Stuckey, J.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	P30CA046592

Revision History  

• Version 1.0: 2024-10-02
  Type: Initial release
  
• Version 1.1: 2025-03-26
  Changes: Database references, Structure summary