9HTK | pdb_00009htk

Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with glutarimide based compound 2n


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 
    0.210 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.176 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 
    0.178 (Depositor) 

Starting Model: experimental
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Literature

Extending the chemical space of glutarimide-based cereblon ligands through an efficient Rh(II)-catalyzed X-H insertion reaction.

Levashova, E.Bischof, L.Bunev, A.Sapegin, A.Grygor'eva, O.Kudinov, A.Ebeling, S.Tatarinov, I.Dar'in, D.Kantin, G.Hartmann, M.D.Kalinin, S.

(2025) Eur J Med Chem 301: 118235-118235

  • DOI: https://doi.org/10.1016/j.ejmech.2025.118235
  • Primary Citation of Related Structures:  
    9HTK, 9HTL, 9HTM, 9HTN, 9HTO, 9HTP, 9HTQ

  • PubMed Abstract: 

    In this work we present an easy, one-step synthetic protocol to explore a large chemical space of glutarimide-based cereblon (CRBN) ligands for targeted protein degradation. It is built upon our recently suggested approach to generating structurally diverse series of alpha-substituted glutarimide derivatives through an efficient Rh(II)-catalyzed X-H insertion reaction of 3-diazopiperidine-2,6-dione, with moderate to high yields. In total, 25 glutarimide derivatives incorporating variable side chains were synthesized and evaluated in vitro. All ligands showed a favorable lipophilicity, and several were able to outperform the binding affinity of thalidomide as a reference. In addition, most compounds showed low intrinsic cytotoxicity in myeloma cell lines and human peripheral blood mononuclear cells, and did not recruit canonical neosubstrates. A cellular thermal shift assay further demonstrated that the most potent analogs stabilize CRBN in live cells, confirming their on-target engagement. The development of the series was accompanied by a crystallographic study, which rationalizes the observed improvements in binding affinity and neosubstrate selectivity, and can support further development towards molecular glue activity and PROTACs design.


  • Organizational Affiliation
    • Institute of Chemistry, Saint Petersburg State University, Saint Petersburg, Russia.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cereblon isoform 4
A, B, C
125Magnetospirillum gryphiswaldenseMutation(s): 0 
Gene Names: MGR_0879
UniProt
Find proteins for A4TVL0 (Magnetospirillum gryphiswaldense)
Explore A4TVL0 
Go to UniProtKB:  A4TVL0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA4TVL0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1IXA (Subject of Investigation/LOI)
Query on A1IXA

Download Ideal Coordinates CCD File 
E [auth A],
I [auth C]
(3S)-3-phenylsulfanylpiperidine-2,6-dione
C11 H11 N O2 S
DVTWEZHTLIJLKO-VIFPVBQESA-N
A1I4R
Query on A1I4R

Download Ideal Coordinates CCD File 
G [auth B](3R)-3-phenylsulfanylpiperidine-2,6-dione
C11 H11 N O2 S
DVTWEZHTLIJLKO-SECBINFHSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B],
H [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free:  0.210 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.176 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 0.178 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.609α = 90
b = 59.756β = 90
c = 88.464γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-29
    Type: Initial release