9Y7D: Cereblon with Golcadomide and Ikaros ZF1-2-3

Cereblon with Golcadomide and Ikaros ZF1-2-3. Determined by electron microscopy at 3.26 Å resolution. Released 15 Oct 2025.

Method: Electron microscopy
Resolution: 3.26 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,183
Mol. weight: 59.87 kDa
Ligands: A1AF4, ZN
Released: 15 Oct 2025

Explore 9Y7D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9Y7D contains 12 α-helices and 23 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain B: 11 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	78-80	3	1
β-strand	83	1	1
β-strand	96-101	6	1
α-helix	104-115	12
β-strand	119-125	7	1
β-strand	133-146	14	1
β-strand	155-169	15	1
β-strand	172	1	1
β-strand	178	1	1
β-strand	181-184	4	1
α-helix	185-186	2
α-helix	208-212	5
α-helix	221-231	11
α-helix	233-236	4
α-helix	242-247	6
α-helix	250-261	12
α-helix	277-285	9
α-helix	292-300	9
α-helix	304-316	13
β-strand	322-323	2	2
α-helix	330-332	3
β-strand	337	1	3
β-strand	346-347	2	3
β-strand	350	1	4
β-strand	356	1	4
β-strand	359-362	4	3
β-strand	368-370	3	5
β-strand	375	1	6
β-strand	386	1	6
β-strand	389-391	3	5
β-strand	397	1	5
β-strand	400-401	2	3
β-strand	415-418	4	3
β-strand	422-423	2	2

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	157-168	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein cereblon	B	protein	406	Homo sapiens	Q96SW2 (AlphaFold model)
DNA-binding protein Ikaros	C	protein	115	Homo sapiens	Q13422 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>9Y7D_1 Protein cereblon (chains B)
GSMEAKKPNIINFDTSLPTSHTYLGADMEEFHGRTLHDDDSCQVIPVLPQVMMILIPGQT
LPLQLFHPQEVSMVRNLIQKDRTFAVLAYSNVQEREAQFGTTAEIYAYREEQDFGIEIVK
VKAIGRQRFKVLELRTQSDGIQQAKVQILPECVLPSTMSAVQLESLNKCQIFPSKPVSRE
DQCSYKWWQKYQKRKFHCANLTSWPRWLYSLYDAETLMDRIKKQLREWDENLKDDSLPSN
PIDFSYRVAACLPIDDVLRIQLLKIGSAIQRLRCELDIMNKCTSLCCKQCQETEITTKNE
IFSLSLCGPMAAYVNPHGYVHETLTVYKACNLNLIGRPSTEHSWFPGYAWTVAQCKICAS
HIGWKFTATKKDMSPQKFWGLTRSALLPTIPDTEDEISPDKVILCL

Sequence of entity 2 (C), FASTA

>9Y7D_2 DNA-binding protein Ikaros (chains C)
GRMLDASGEKMNGSHRDQGSSALSGVGGIRLPNGKLKCDICGIICIGPNVLMVHKRSHTG
ERPFQCNQCGASFTQKGNLLRHIKLHSGEKPFKCHLCNYACRRRDALTGHLRTHS

Ligands and cofactors

ID	Name	Formula	Copies
A1AF4	Golcadomide	C28 H30 F N5 O5	1
ZN	Zinc ion	Zn	2

Primary citation

Golcadomide: An Oral CELMoD Agent Targeting IKZF1/3 for Diffuse Large B-cell Lymphoma. Mo, Z., Groocock, L., Wood, S. et al. Blood Cancer Discov (2026) 7:104-128. DOI 10.1158/2643-3230.BCD-25-0059 · PubMed

Other PDB entries of the same protein (UniProt Q96SW2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4M91 1.1 Å, crystal structure of hN33/Tusc3-peptide 1
9CUO 1.6 Å, Crystal structure of CRBN with compound 3
9OHQ 1.6 Å, Structure of CRBN:IKZF2:Compound 15
9DOM 1.69 Å, PVTX-405: A Potent, Highly Selective, and Orally Efficacious Molecular Glue Degrader of…
7BQV 1.8 Å, Cereblon in complex with SALL4 and (S)-5-hydroxythalidomide
9O91 1.86 Å, Structure of IKZF2:CRBN:Compound 5 ternary structure
7BQU 1.9 Å, Cereblon in complex with SALL4 and (S)-thalidomide
9GAO 1.95 Å, Crystal structure of CRBNmidi in complex with 2-(4-(2,6-dioxopiperidin-3-yl)phenoxy)-N-me…
9FJX 2.0 Å, Crystal structure of human CRBN-DDB1 in complex with Lenalidomide
8RQC 2.15 Å, Crystal structure of CRBN-midi in complex with mezigdomide and IKZF1 ZF2
8RQ8 2.19 Å, Crystal structure of CRBN-midi in complex with mezigdomide
9OHR 2.34 Å, Structure of CRBN:IKZF2:Compound 35

Browse structure collections

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