8AOQ

Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 20a


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.195 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Synthesis of novel glutarimide ligands for the E3 ligase substrate receptor Cereblon (CRBN): Investigation of their binding mode and antiproliferative effects against myeloma cell lines.

Krasavin, M.Adamchik, M.Bubyrev, A.Heim, C.Maiwald, S.Zhukovsky, D.Zhmurov, P.Bunev, A.Hartmann, M.D.

(2023) Eur J Med Chem 246: 114990-114990

  • DOI: https://doi.org/10.1016/j.ejmech.2022.114990
  • Primary Citation of Related Structures:  
    8AOP, 8AOQ

  • PubMed Abstract: 

    To expand the chemical toolkit for targeted protein degradation, we report the generation of a new series of non-thalidomide Cereblon (CRBN) ligands. Readily available 2-methylidene glutarimide was converted to a series of 2-((hetero)aryl(methyl))thio glutarimides via the thio-Michael addition reaction. The compounds thus synthesized were evaluated for their affinity to the thalidomide-binding domain of human CRBN and their binding modes studied via X-ray crystallography. This helped identify several promising glutarimide derivatives which bind stronger to CRBN compared to thalidomide and contain a functional group which permits further chemical conjugation. Oxidation of the sulfur atom in a select group of 2-((hetero)aryl(methyl))thio glutarimides produced the respective sulfones which were found to possess a markedly stronger antiproliferative profile against multiple myeloma cell lines and a sophisticated structural binding mode with additional hydrogen bonding interactions. The newly identified Cereblon ligands form the basis for the synthesis of novel PROTAC protein degraders.


  • Organizational Affiliation

    Saint Petersburg State University, Saint Petersburg, 199034, Russian Federation; Immanuel Kant Baltic Federal University, Kaliningrad, 236041, Russian Federation. Electronic address: m.krasavin@spbu.ru.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cereblon isoform 4
A, B, C
124Magnetospirillum 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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.66α = 90
b = 59.169β = 90
c = 88.334γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling

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: 2023-01-11
    Type: Initial release
  • Version 1.1: 2024-02-07
    Changes: Data collection, Refinement description