9Y7D | pdb_00009y7d

Cereblon with Golcadomide and Ikaros ZF1-2-3

• PDB DOI: https://doi.org/10.2210/pdb9Y7D/pdb
• EM Map EMD-43788: EMDB EMDataResource
• EM Map EMD-72653: EMDB EMDataResource

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda, Escherichia coli
• Mutation(s): No 


• Deposited: 2025-09-09 Released: 2025-10-15 
• Deposition Author(s): Watson, E.R., Lander, G.C.
• Funding Organization(s): Other private

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Experimental Data Snapshot

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

Literature

Discovery of Golcadomide (CC-99282) as a promising drug candidate for diffuse large B-cell lymphoma

Watson, E.R.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein cereblon	A [auth B]	406	Homo sapiens	Mutation(s): 0  Gene Names: CRBN, AD-006
UniProt & NIH Common Fund Data Resources
Find proteins for Q96SW2 (Homo sapiens) Explore Q96SW2  Go to UniProtKB:  Q96SW2
PHAROS:  Q96SW2 GTEx:  ENSG00000113851

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-binding protein Ikaros	B [auth C]	115	Homo sapiens	Mutation(s): 0  Gene Names: IKZF1, IK1, IKAROS, LYF1, ZNFN1A1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13422 (Homo sapiens) Explore Q13422  Go to UniProtKB:  Q13422
PHAROS:  Q13422 GTEx:  ENSG00000185811

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1AF4 (Subject of Investigation/LOI)	D [auth B]	Golcadomide C28 H30 F N5 O5 NZYDBVQXOGPDDU-QHCPKHFHSA-N
ZN	C [auth B], E [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

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

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-15 
Deposition Author(s): Watson, E.R., Lander, G.C.

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Funding Organization	Location	Grant Number
Other private	United States	--

Revision History  

• Version 1.0: 2025-10-15
  Type: Initial release