9R1P | pdb_00009r1p

Crystal structure of STUB1 complexed with a compound molecule


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 
    0.234 (Depositor), 0.239 (DCC) 
  • R-Value Work: 
    0.205 (Depositor), 0.215 (DCC) 
  • R-Value Observed: 
    0.207 (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

A rapid imaging-based screen for induced-proximity degraders identifies a potent degrader of oncoprotein SKP2.

Chu, Y.Chen, S.Yang, M.Chen, Y.Fang, H.Huang, P.Xie, Y.Sun, C.Chen, Y.Zhang, B.Li, L.Mu, H.Song, D.Cheng, W.Wang, C.Jiang, W.Xu, X.He, Z.Chen, S.Liu, M.Ma, J.Yang, M.Cao, J.Gao, J.Shen, J.Zhang, L.Bai, Y.Liu, Z.Chen, J.Dai, S.Zeng, Y.A.Zhao, Y.Zhou, H.Chen, C.Ru, H.Tan, L.Chi, X.Wang, F.Gao, D.Lin, M.Deng, X.Jiang, H.

(2025) Nat Biotechnol 

  • DOI: https://doi.org/10.1038/s41587-025-02793-8
  • Primary Citation of Related Structures:  
    9R1P

  • PubMed Abstract: 

    Targeted protein degraders hold potential as therapeutic agents to target conventionally 'undruggable' proteins. Here, we develop a high-throughput screen, DEath FUSion Escaper (DEFUSE), to identify small-molecule protein degraders. By conjugating the protein of interest to a fast-acting triggerable death protein, this approach translates target protein degradation into a cell survival phenotype to illustrate the presence of degraders. Using this method, we discovered a small molecule (SKPer1) that triggers degradation of the oncoprotein SKP2 and specifically kills SKP2-expressing cancer cells. Mechanistically, SKPer1 acts as an induced-proximity degrader by inducing interaction between SKP2 and an E3 ligase, STUB1, resulting in SKP2 ubiquitination and degradation. SKPer1 exhibits substantial tumour suppression with good safety profiles in vivo. We further show that a sequence of ten amino acids from SKP2 can serve as a versatile degradation tag.


  • Organizational Affiliation
    • Key Laboratory of RNA Innovation, Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase CHIP140Homo 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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1JBJ (Subject of Investigation/LOI)
Query on A1JBJ

Download Ideal Coordinates CCD File 
B [auth A]1-[3-[1-methyl-4-(pyridin-3-ylmethylamino)pyrazolo[3,4-d]pyrimidin-6-yl]phenyl]-3-[3-(trifluoromethyl)phenyl]thiourea
C26 H21 F3 N8 S
UPEIYMKISINCQK-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free:  0.234 (Depositor), 0.239 (DCC) 
  • R-Value Work:  0.205 (Depositor), 0.215 (DCC) 
  • R-Value Observed: 0.207 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.948α = 90
b = 89.948β = 90
c = 53.597γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-17
    Type: Initial release