9HNE | pdb_00009hne

Cereblon in complex with DDB1, GSPT1 and Compound-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.90 Å
  • R-Value Free: 
    0.336 (Depositor), 0.327 (DCC) 
  • R-Value Work: 
    0.259 (Depositor), 0.256 (DCC) 
  • R-Value Observed: 
    0.262 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Targeted degradation of GSPT1 and NEK7 by a molecular glue prodrug for treatment of HCC.

Glaza, P.Pluta, R.Odrzywol, K.E.Klejnot, M.Wieczorek, M.Cottens, S.Coppen, D.Dobrzanski, P.Drmota, T.Lis-Grzesniak, J.Sniezewska, A.Majkut, J.Mianowska, M.Rozborska, P.Jarmuszkiewicz, M.Kaczanowska, K.Adamska, A.Takagi, T.Sawicka, A.Serwotka-Suszczak, A.Makowska, O.Gajewska, D.Jurczak, K.Leszkowicz, K.Mankiewicz, M.Przytulski, K.Wisniewski, J.Szlachcic, A.Walczak, M.J.

(2025) Commun Chem 8: 247-247

  • DOI: https://doi.org/10.1038/s42004-025-01641-9
  • Primary Citation of Related Structures:  
    9HNE

  • PubMed Abstract: 

    Targeted Protein Degradation (TPD) technology, in the form of CRBN-modulating molecular glues, offers numerous unprecedented therapeutic benefits as evidenced by the success of approved high-value immunomodulatory imide drugs (IMiDs) such as lenalidomide and pomalidomide. Building upon these successes, we employed a small CRBN-focused library of molecular glues in a phenotypic screen against hepatocellular carcinoma (HCC) cell lines. While the original library was primarily designed to target SALL4, we identified additional CRBN substrates, including GSPT1, NEK7, and CK1α, whose degradation potently induced cell death in HCC cell lines. Subsequent lead optimization efforts yielded a compound, ABS-752, which demonstrated superior in vitro and in vivo activity through the potent degradation of GSPT1. Notably, ABS-752 does not form ternary complexes with CRBN and the neosubstrates. Further investigations revealed that ABS-752 is a prodrug activated by the monoamine oxidase, VAP-1, to an aldehyde intermediate and subsequently to the active molecule, ABT-002. VAP-1, which is overexpressed in cirrhotic liver, was identified as the primary monoamine oxidase responsible for the conversion of ABS-752. ABS-752 is currently in clinical trials for the treatment of HCC.


  • Organizational Affiliation
    • Captor Therapeutics Inc., Duńska St 11, PL54427, Wrocław, Poland.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic peptide chain release factor GTP-binding subunit ERF3A
A, D
197Homo sapiensMutation(s): 0 
Gene Names: GSPT1ERF3A
EC: 3.6.5
UniProt & NIH Common Fund Data Resources
Find proteins for P15170 (Homo sapiens)
Explore P15170 
Go to UniProtKB:  P15170
PHAROS:  P15170
GTEx:  ENSG00000103342 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15170
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA damage-binding protein 1
B, E
1,140Homo sapiensMutation(s): 0 
Gene Names: DDB1XAP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q16531 (Homo sapiens)
Explore Q16531 
Go to UniProtKB:  Q16531
PHAROS:  Q16531
GTEx:  ENSG00000167986 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16531
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Protein cereblon
C, F
404Homo sapiensMutation(s): 0 
Gene Names: CRBNAD-006
UniProt & NIH Common Fund Data Resources
Find proteins for Q96SW2 (Homo sapiens)
Explore Q96SW2 
Go to UniProtKB:  Q96SW2
PHAROS:  Q96SW2
GTEx:  ENSG00000113851 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96SW2
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.90 Å
  • R-Value Free:  0.336 (Depositor), 0.327 (DCC) 
  • R-Value Work:  0.259 (Depositor), 0.256 (DCC) 
  • R-Value Observed: 0.262 (Depositor) 
Space Group: P 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 158.34α = 90
b = 112.38β = 95.25
c = 177.94γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privatePoland--

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-22
    Type: Initial release