9OHR | pdb_00009ohr

Structure of CRBN:IKZF2:Compound 35

PDB DOI: https://doi.org/10.2210/pdb9OHR/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-05-05 Released: 2025-09-03
Deposition Author(s): Strickland, C.O., Rice, C.T.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.34 Å
R-Value Free:
0.290 (Depositor), 0.290 (DCC)
R-Value Work:
0.224 (Depositor), 0.230 (DCC)
R-Value Observed:
0.228 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Discovery of a Novel Series of iso -Indolinone-Based Glutarimides as Highly Efficacious and Selective IKZF2 Molecular Glue Degraders.

Zhang, X., Dhruv, H., Deng, Q., Tudor, M., Bechtel, N., Nagilla, R., Jolivette, L., Rice, C.T., Orth, P., Behshad, E., Strickland, C., Mohammad, H.P., Bai, L., McEachern, D., Wang, S., Sui, Z., Priestley, E.S.

(2025) J Med Chem 68: 18230-18257

PubMed: 40842140 Search on PubMed
DOI: https://doi.org/10.1021/acs.jmedchem.5c00668
Primary Citation of Related Structures:
9OHQ, 9OHR

PubMed Abstract:
Immunosuppressive Tregs, regulated by IKZF2 (Helios), promote tumor immune evasion and resistance to immune checkpoint therapies (ICTs). Targeting IKZF2 degradation offers a promising cancer immunotherapy approach. We developed a novel series of iso -indolinone-based glutarimides, identifying compound 55 as a potent, selective IKZF2 degrader with >90% D _max in Jurkat cells, outperforming benchmarks DKY709 and PVTX-405. It exhibits strong selectivity over IMiD neo-substrates, favorable solubility, metabolic stability, and oral bioavailability in rodents. PK/PD studies confirmed profound, persistent IKZF2 degradation in mouse spleen and thymus after a single oral dose. As a promising early-stage tool, 55 provides a foundation for further preclinical evaluation in cancer immunotherapy.

Organizational Affiliation

SK Life Sciences Laboratories, 2500 Renaissance Boulevard, King of Prussia, Pennsylvania 19406, United States.

Macromolecule Content

Total Structure Weight: 65.03 kDa
Atom Count: 4,405
Modeled Residue Count: 546
Deposited Residue Count: 564
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein cereblon	A, C, E, G	111	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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q96SW2
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Zinc finger protein Helios	B, D, F, H	30	Homo sapiens	Mutation(s): 0 Gene Names: IKZF2, HELIOS, ZNFN1A2
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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9UKS7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1CBG (Subject of Investigation/LOI) Query on A1CBG Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain L [auth C] SDF format, chain R [auth G] SDF format, chain O [auth E] MOL2 format, chain I [auth A] MOL2 format, chain L [auth C] MOL2 format, chain R [auth G] MOL2 format, chain O [auth E] mmCIF format, chain I [auth A] mmCIF format, chain L [auth C] mmCIF format, chain R [auth G] mmCIF format, chain O [auth E]	I [auth A], L [auth C], O [auth E], R [auth G]	(3S)-3-[(5M)-5-{1-(oxetan-3-yl)-4-[(pyrrolidin-1-yl)methyl]-1H-pyrrolo[2,3-b]pyridin-6-yl}-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione C₂₈ H₂₉ N₅ O₄ OZSNWUQQBQCHTP-DEOSSOPVSA-N		Interactions Focus chain I [auth A] Focus chain L [auth C] Focus chain O [auth E] Focus chain R [auth G] Interactions & Density Focus chain I [auth A] Focus chain L [auth C] Focus chain O [auth E] Focus chain R [auth G]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain M [auth C] SDF format, chain N [auth D] SDF format, chain P [auth E] SDF format, chain T [auth G] SDF format, chain U [auth H] SDF format, chain S [auth G] SDF format, chain Q [auth F] SDF format, chain J [auth A] MOL2 format, chain K [auth B] MOL2 format, chain M [auth C] MOL2 format, chain N [auth D] MOL2 format, chain P [auth E] MOL2 format, chain T [auth G] MOL2 format, chain U [auth H] MOL2 format, chain S [auth G] MOL2 format, chain Q [auth F] MOL2 format, chain J [auth A] mmCIF format, chain K [auth B] mmCIF format, chain M [auth C] mmCIF format, chain N [auth D] mmCIF format, chain P [auth E] mmCIF format, chain T [auth G] mmCIF format, chain U [auth H] mmCIF format, chain S [auth G] mmCIF format, chain Q [auth F] mmCIF format, chain J [auth A]	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 G], U [auth H]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth D] Focus chain P [auth E] Focus chain Q [auth F] Focus chain S [auth G] Focus chain T [auth G] Focus chain U [auth H] Interactions & Density Focus chain J [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth D] Focus chain P [auth E] Focus chain Q [auth F] Focus chain S [auth G] Focus chain T [auth G] Focus chain U [auth H]