Cereblon isoform 4 in complex with novel Benzamide-Type Cereblon Binder 11c

Experimental Data Snapshot

  • Resolution: 1.84 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.184 

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Leveraging Ligand Affinity and Properties: Discovery of Novel Benzamide-Type Cereblon Binders for the Design of PROTACs.

Steinebach, C.Bricelj, A.Murgai, A.Sosic, I.Bischof, L.Ng, Y.L.D.Heim, C.Maiwald, S.Proj, M.Voget, R.Feller, F.Kosmrlj, J.Sapozhnikova, V.Schmidt, A.Zuleeg, M.R.Lemnitzer, P.Mertins, P.Hansen, F.K.Gutschow, M.Kronke, J.Hartmann, M.D.

(2023) J Med Chem 66: 14513-14543

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c00851
  • Primary Citation of Related Structures:  
    8OU3, 8OU4, 8OU5, 8OU6, 8OU7, 8OU9, 8OUA

  • PubMed Abstract: 

    Immunomodulatory imide drugs (IMiDs) such as thalidomide, pomalidomide, and lenalidomide are the most common cereblon (CRBN) recruiters in proteolysis-targeting chimera (PROTAC) design. However, these CRBN ligands induce the degradation of IMiD neosubstrates and are inherently unstable, degrading hydrolytically under moderate conditions. In this work, we simultaneously optimized physiochemical properties, stability, on-target affinity, and off-target neosubstrate modulation features to develop novel nonphthalimide CRBN binders. These efforts led to the discovery of conformationally locked benzamide-type derivatives that replicate the interactions of the natural CRBN degron, exhibit enhanced chemical stability, and display a favorable selectivity profile in terms of neosubstrate recruitment. The utility of the most potent ligands was demonstrated by their transformation into potent degraders of BRD4 and HDAC6 that outperform previously described reference PROTACs. Together with their significantly decreased neomorphic ligase activity on IKZF1/3 and SALL4, these ligands provide opportunities for the design of highly selective and potent chemically inert proximity-inducing compounds.

  • Organizational Affiliation

    Interfaculty Institute of Biochemistry, University of Tübingen, D-72076 Tübingen, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cereblon isoform 4
A, B, C
105Magnetospirillum gryphiswaldense MSR-1 v2Mutation(s): 0 
Gene Names: MGR_0879
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
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
W26 (Subject of Investigation/LOI)
Query on W26

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B]
C13 H15 N3 O3
Query on PO4

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
J [auth B],
K [auth C]
O4 P
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A],
H [auth B],
L [auth C]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.84 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.184 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.989α = 90
b = 59.126β = 90
c = 87.139γ = 90
Software Package:
Software NamePurpose
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: 2023-11-15
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Database references