9BIG | pdb_00009big

Stat6 bound to degrader AK-1690


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
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


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

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c01009
  • Primary Citation of 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.


  • Organizational Affiliation
    • Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Signal transducer and activator of transcription 6546Homo sapiensMutation(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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42226
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1AQQ (Subject of Investigation/LOI)
Query on A1AQQ

Download Ideal Coordinates CCD File 
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 = 103.505α = 90
b = 103.505β = 90
c = 53.059γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesP30CA046592

Revision History  (Full details and data files)

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