9QF1 | pdb_00009qf1

Structure of CHIP E3 ubiquitin ligase TPR domain in complex with compound 2

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

  • Deposited: 2025-03-11 Released: 2025-08-27 
  • Deposition Author(s): Breed, J.
  • Funding Organization(s): Other private

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free: 
    0.219 (Depositor), 0.218 (DCC) 
  • R-Value Work: 
    0.196 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 
    0.197 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Discovery of Small-Molecule Ligands for the E3 Ligase STUB1/CHIP from a DNA-Encoded Library Screen.

Lucas, S.C.C.Milbradt, A.G.Breed, J.De Genst, E.Jackson, A.Solovyeva, A.Ackroyd, B.Bauer, M.R.Liu, J.Longmire, D.Petrovic, D.Rivers, E.L.Stubbs, C.Winlow, P.Bazzaz, S.Dickson, P.Gikunju, D.Guie, M.A.Guilinger, J.P.Hupp, C.D.Jetson, R.Keefe, A.D.Nugai, K.Yeoman, J.T.S.Zhang, Y.Feng, X.Yu, D.Phillips, C.

(2025) ACS Med Chem Lett 16: 1445-1451

  • DOI: https://doi.org/10.1021/acsmedchemlett.5c00361
  • Primary Citation of Related Structures:  
    9QEU, 9QF1, 9QFS, 9QFY

  • PubMed Abstract: 

    STIP1 homology and U-box containing protein 1 (STUB1), also known as the C-terminus of Hsc70-interacting protein (CHIP), is an E3 ligase that plays a crucial role in removal of misfolded proteins via Hsc70. A DEL screen was run against CHIP to identify small-molecule binders. Two hits were identified that were confirmed by biochemical and biophysical techniques, including 2D NMR. X-ray crystal structures were obtained, which revealed binding to the peptide binding site. Fragment-based deconstruction indicated that hit 2 was a suitable starting point for optimization. During the optimization, an unexpected rearrangement of an oxadiazole from an array hit led to the exploration of an amide vector. This resulted in the discovery of compound 5 , which is the most potent small-molecule ligand for CHIP identified to date and a suitable starting point for further optimization into a tool molecule or PROTAC warhead.


  • Organizational Affiliation

    Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase CHIP136Homo sapiensMutation(s): 0 
Gene Names: STUB1CHIPPP1131
EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UNE7 (Homo sapiens)
Explore Q9UNE7 
Go to UniProtKB:  Q9UNE7
PHAROS:  Q9UNE7
GTEx:  ENSG00000103266 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UNE7
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1I5T (Subject of Investigation/LOI)
Query on A1I5T

Download Ideal Coordinates CCD File 
B [auth A]~{N}-methyl-~{N}-[(1~{R})-1-pyridin-2-yl-3-pyrrolidin-1-yl-propyl]-5-[4,5,6,7-tetrakis(fluoranyl)-1~{H}-indol-3-yl]-1,3,4-oxadiazol-2-amine
C23 H22 F4 N6 O
IUWAZBMFUACYBK-OAHLLOKOSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free:  0.219 (Depositor), 0.218 (DCC) 
  • R-Value Work:  0.196 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 0.197 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.108α = 90
b = 71.264β = 90
c = 75.945γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
BUSTERrefinement
XDSdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2025-08-27 
  • Deposition Author(s): Breed, J.

Funding OrganizationLocationGrant Number
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-27
    Type: Initial release