7PJK

Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with a benzotriazole analog of thalidomide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.211 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Replacing the phthalimide core in thalidomide with benzotriazole.

Krasavin, M.Bubyrev, A.Kazantsev, A.Heim, C.Maiwald, S.Zhukovsky, D.Dar'in, D.Hartmann, M.D.Bunev, A.

(2022) J Enzyme Inhib Med Chem 37: 527-530

  • DOI: https://doi.org/10.1080/14756366.2021.2024525
  • Primary Citation of Related Structures:  
    7PJK

  • PubMed Abstract: 

    The advent of proteolysis-targeting chimaeras (PROTACs) mandates that new ligands for the recruitment of E3 ligases are discovered. The traditional immunomodulatory drugs (IMiDs) such as thalidomide and its analogues (all based on the phthalimide glutarimide core) bind to Cereblon, the substrate receptor of the CRL4A CRBN E3 ligase. We designed a thalidomide analogue in which the phthalimide moiety was replaced with benzotriazole, using an innovative synthesis strategy. Compared to thalidomide, the resulting "benzotriazolo thalidomide" has a similar binding mode, but improved properties, as revealed in crystallographic analyses, affinity assays and cell culture.


  • 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 gryphiswaldense MSR-1Mutation(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: 1.99 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.211 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.779α = 90
b = 59.435β = 90
c = 88.189γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
REFMACphasing

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: 2022-03-16
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description