9O91 | pdb_00009o91

Structure of IKZF2:CRBN:Compound 5 ternary structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 
    0.218 (Depositor), 0.227 (DCC) 
  • R-Value Work: 
    0.175 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 
    0.177 (Depositor) 

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Ligand Structure Quality Assessment 


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Literature

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.Tudor, M.Nagilla, R.Jolivette, L.J.Rice, C.T.Orth, P.Behshad, E.Strickland, C.O.Mohammad, H.P.Sui, Z.Priestley, E.S.

(2025) Bioorg Med Chem Lett 124: 130263-130263

  • DOI: https://doi.org/10.1016/j.bmcl.2025.130263
  • Primary Citation of Related Structures:  
    9O91

  • PubMed Abstract: 

    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.


  • Organizational Affiliation
    • SK Life Sciences Labs, 2500 Renaissance Blvd, King of Prussia, PA 19406, United States. Electronic address: XZhang@sklslabs.com.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein cereblon
A, C, E, G
111Homo sapiensMutation(s): 4 
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:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Zinc finger protein Helios
B, D, F, H
30Homo sapiensMutation(s): 0 
Gene Names: IKZF2HELIOSZNFN1A2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UKS7 (Homo sapiens)
Explore Q9UKS7 
Go to UniProtKB:  Q9UKS7
PHAROS:  Q9UKS7
GTEx:  ENSG00000030419 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UKS7
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1CAC (Subject of Investigation/LOI)
Query on A1CAC

Download Ideal Coordinates CCD File 
I [auth A],
L [auth C],
O [auth E],
R [auth G]
(3S)-3-[(5M)-1-oxo-5-{4-[(pyrrolidin-1-yl)methyl]-1H-pyrrolo[2,3-b]pyridin-6-yl}-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione
C25 H25 N5 O3
SNZGVVSAMPFNLQ-NRFANRHFSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
J [auth A]
K [auth B]
M [auth C]
N [auth D]
P [auth E]
J [auth A],
K [auth B],
M [auth C],
N [auth D],
P [auth E],
Q [auth F],
S [auth G],
T [auth H]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free:  0.218 (Depositor), 0.227 (DCC) 
  • R-Value Work:  0.175 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 0.177 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.16α = 90
b = 70.18β = 90.01
c = 78.71γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-09
    Type: Initial release