9O91: IKZF2:CRBN:Compound 5 ternary structure

Structure of IKZF2:CRBN:Compound 5 ternary structure. Determined by X-ray diffraction at 1.86 Å resolution. Released 9 Jul 2025.

Method: X-ray diffraction
Resolution: 1.86 Å
Organism: Homo sapiens
Chains: 8
Atoms: 4,683
Mol. weight: 64.74 kDa
Ligands: ZN, A1CAC
Released: 9 Jul 2025

Explore 9O91 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9O91 contains 12 α-helices and 48 β-strands across 8 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.

Chains A, C, E and G: 2 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	320-323	4	1
β-strand	330-333	4	1
α-helix	334-336	3
β-strand	337	1	2
β-strand	346-350	5	2
β-strand	356-362	7	2
β-strand	368-375	8	2
β-strand	384-391	8	2
β-strand	397-404	8	2
β-strand	413-418	6	2
α-helix	419-421	3
β-strand	422-423	2	1

Chains B, D, F and H: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
β-strand	140-141	2	3
β-strand	148-149	2	3
α-helix	152-161	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein cereblon	A, C, E, G	protein	111	Homo sapiens	Q96SW2 (AlphaFold model)
Zinc finger protein Helios	B, D, F, H	protein	30	Homo sapiens	Q9UKS7 (AlphaFold model)

Sequence of entity 1 (A, C, E, G), FASTA

>9O91_1 Protein cereblon (chains A, C, E, G)
GPSTSLSCKQCQETEITTKNEIFSLSLSGPMAAYVNPHGYVHETLTVYKASNLNLIGRPS
TEHSWFPGYAWTVAQCKICASHIGWKFTATKKDMSPQKFWGLTRSALLPTI

Sequence of entity 2 (B, D, F, H), FASTA

>9O91_2 Zinc finger protein Helios (chains B, D, F, H)
GGERPFHCNQCGASFTQKGNLLRHIKLHSG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	8
A1CAC	(3S)-3-[(5M)-1-oxo-5-{4-[(pyrrolidin-1-yl)methyl]-1H-pyrrolo[2,3-b]pyridin-6-yl…	C25 H25 N5 O3	4

Primary citation

Overcoming CK1 alpha liability in the discovery of a series of isoIndolinone Glutarimides as selective IKZF2 molecular glue degraders. Zhang, X., Deng, Q., Dhruv, H. et al. Bioorg Med Chem Lett (2025) 124:130263-130263. DOI 10.1016/j.bmcl.2025.130263 · 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
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
9SFM 2.39 Å, Crystal structure of Cereblon-DDB1 in complex with SB-405483 and Lenalidomide

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