9O91 image
Deposition Date 2025-04-17
Release Date 2025-07-09
Last Version Date 2025-07-09
Entry Detail
PDB ID:
9O91
Keywords:
Title:
Structure of IKZF2:CRBN:Compound 5 ternary structure
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Host Organism:
Method Details:
Experimental Method:
Resolution:
1.86 Å
R-Value Free:
0.21
R-Value Work:
0.17
R-Value Observed:
0.17
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Protein cereblon
Gene (Uniprot):CRBN
Chain IDs:A, C, E, G
Chain Length:111
Number of Molecules:4
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Zinc finger protein Helios
Gene (Uniprot):IKZF2
Chain IDs:B, D, F, H
Chain Length:30
Number of Molecules:4
Biological Source:Homo sapiens
Primary Citation
Overcoming CK1 alpha liability in the discovery of a series of isoIndolinone Glutarimides as selective IKZF2 molecular glue degraders.
Bioorg.Med.Chem.Lett. 124 130263 130263 (2025)
PMID: 40334997 DOI: 10.1016/j.bmcl.2025.130263

Abstact

IKZF2 (Ikaros Family Zinc Finger 2) is a transcription factor implicated in immune regulation and hematologic malignancies, where its dysregulation drives oncogenic programs, immune evasion, and therapy resistance. While targeted protein degradation (TPD) has emerged as a promising strategy, achieving selective IKZF2 degradation remains challenging due to off-target effects on structurally related neosubstrates such as IKZF1/3, SALL4, CK1α, and GSPT1. Here, we report the discovery of a novel series of isoindolinone glutarimide-based molecular glue degraders that selectively degrade IKZF2 while sparing CK1α and other neosubstrates. Through a structure-guided medicinal chemistry campaign, we identified divergent structure-activity relationships (SARs) enabling potent IKZF2 degradation with minimal off-target activity. The lead degrader (31) demonstrated high selectivity between IKZF2 and CK1α with acceptable oral bioavailability in mice. Our findings highlight the feasibility of developing precise IKZF2 degraders and provide a framework for optimizing selectivity in molecular glue design, offering a potential therapeutic strategy for IKZF2-dependent cancers. 2025 Elsevier Ltd. All rights reserved.

Legend

Protein

Chemical

Disease

Primary Citation of related structures