9DQD | pdb_00009dqd

cryo-EM structure of human Cereblon/DDB1 in complex with a non-traditional CRBN binder


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Development of a Buchwald-Hartwig Amination for an Accelerated Library Synthesis of Cereblon Binders.

Lejava, A.Miseo, G.A.Phan, T.Zhu, J.Powers, H.L.Li, J.Mortensen, D.S.Zapf, C.W.Khambatta, G.Buenviaje, J.Holmberg-Douglas, N.

(2025) ACS Med Chem Lett 16: 89-95

  • DOI: https://doi.org/10.1021/acsmedchemlett.4c00462
  • Primary Citation of Related Structures:  
    9DQD

  • PubMed Abstract: 

    In recent years, targeted protein degradation (TPD) has emerged as a powerful therapeutic modality utilizing both heterobifunctional ligand-directed degraders (LDDs) and molecular glues (e.g., CELMoDs) to recruit E3 ligases for inducing polyubiquitination and subsequent proteasomal degradation of target proteins. The immunomodulatory drugs lenalidomide and pomalidomide bind to cereblon (CRBN), a substrate receptor of the CRL4A E3 ligase complex, to initiate degradation of neosubstrates critical for cell survival. Recently, nonlenalidomide or pomalidomide CRBN binders, known as alternate glutarimides, have gained popularity, offering potential degraders with varying physicochemical properties. Specifically, 3-substituted indazole derivatives have emerged as potent CRBN binders. We developed conditions for the direct cross-coupling of unprotected glutarimides with amines, streamlining the synthesis of alternative CRBN binders. This manuscript describes the rapid synthesis of 30 CRBN binders, their characterization as potential degraders and a cryo-EM structure of the CRBN/DDB1 with a representative compound ( 6 ).


  • Organizational Affiliation
    • Bristol Myers Squibb, 10300 Campus Point Drive, Suite 100, San Diego, California 92121, United States.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein cereblon467Homo 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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA damage-binding protein 1836Homo 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
Expand
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-25
    Type: Initial release
  • Version 1.1: 2025-01-29
    Changes: Data collection, Database references