9Y7D | pdb_00009y7d

Cereblon with Golcadomide and Ikaros ZF1-2-3


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.26 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9Y7D

This is version 1.1 of the entry. See complete history

Literature

Golcadomide: An Oral CELMoD Agent Targeting IKZF1/3 for Diffuse Large B-cell Lymphoma.

Mo, Z.Groocock, L.Wood, S.Jankeel, D.Mendy, D.Watson, E.R.Kai, Y.Deb, G.Cote, M.Janardhanan, P.Fernandez-Deudero, A.Barnes, L.Peng, S.Groza, M.Kalashnikova, E.Angelo, M.Zhu, J.Galasso, R.Jang, I.S.Castillo, M.S.Fontanillo, C.Polido, G.Christoforou, A.Kercher, T.Lander, G.C.Wang, K.Narla, R.K.Carrancio, S.Pierce, D.W.Rolfe, M.Bence, N.Lopez-Girona, A.

(2026) Blood Cancer Discov 7: 104-128

  • DOI: https://doi.org/10.1158/2643-3230.BCD-25-0059
  • Primary Citation Related Structures: 
    9Y7D

  • PubMed Abstract: 

    Diffuse large B-cell lymphoma (DLBCL) is an aggressive and heterogeneous disease with limited treatment options and a poor prognosis, especially for patients refractory to standard therapies. We report the discovery of golcadomide (CC-99282), an oral cereblon-modulating CELMoD agent designed using target-specific knowledge and optimized pharmacologic properties for the treatment of DLBCL. Golcadomide exhibited rapid, deep, and sustained degradation of transcription factors IKZF1 and IKZF3, surpassing the antitumor activity of the IMiD agent lenalidomide in preclinical models. In human lymphoma cell lines, golcadomide downregulated MYC, activated IFN-stimulated genes, and promoted antiproliferation, apoptosis, and immunogenic cell death. In mouse xenografts, golcadomide preferentially distributed to tissues known to be affected by lymphoma, resulting in enhanced tumor regression and tumor-free outcomes. Pharmacologic and CRISPR screening further revealed genes and pathways underlying golcadomide's antitumor efficacy. These findings supported golcadomide as a promising drug candidate for DLBCL, providing a strong rationale for future golcadomide-based regimens. Golcadomide is an oral cereblon-modulating agent for the treatment of DLBCL. It exhibited rapid, deep, and sustained degradation of IKZF1 and IKZF3, preferentially accumulated in lymphoma residence tissues, and delivered robust antitumor activity. These results provide a strong rationale for continued clinical investigation of golcadomide for patients with DLBCL.


  • Organizational Affiliation
    • Protein Homeostasis (PH) Thematic Research Center (TRC), Bristol Myers Squibb, San Diego, California.

Macromolecule Content 

  • Total Structure Weight: 59.87 kDa 
  • Atom Count: 3,183 
  • Modeled Residue Count: 405 
  • Deposited Residue Count: 521 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein cereblonA [auth B]406Homo 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:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-binding protein IkarosB [auth C]115Homo sapiensMutation(s): 0 
Gene Names: IKZF1IK1IKAROSLYF1ZNFN1A1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13422 (Homo sapiens)
Explore Q13422 
Go to UniProtKB:  Q13422
PHAROS:  Q13422
GTEx:  ENSG00000185811 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13422
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.26 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-15
    Type: Initial release
  • Version 1.1: 2026-04-29
    Changes: Data collection, Database references