9Y5Z | pdb_00009y5z

Crystal structure of ternary complex Helios-ZF2:CRBN:DDB1 in complex with BMS-986449, a molecular glue degrader

PDB DOI: https://doi.org/10.2210/pdb9Y5Z/pdb

Classification: LIGASE
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda, Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-09-05 Released: 2026-09-02
Deposition Author(s): Zhu, J., Pagarigan, B.E., Tran, E.T.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.53 Å
R-Value Free:
0.236 (Depositor), 0.261 (DCC)
R-Value Work:
0.229 (Depositor), 0.249 (DCC)
R-Value Observed:
0.230 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Discovery of BMS-986449: A Potent, Selective Degrader of the Transcription Factors IKZF2 (Helios) and IKZF4 (Eos) to Target Regulatory T Cells in Solid Tumors

Cherney, E.C., Nair, S.K., Penmetsa, S.B.V.K., Shimpukade, B., Huang, A., Bilder, D., Degnan, A.P., Kumi, G.K., Zhang, L., Purandare, A.V., Yang, F., Li, G., Shan, W., Chen, Y., Lin, S., Park, P., Dodd, D.S., Kantheti, D., Padamata, S., Manepalli, R.K.V.L.P., Sirigireddy, N.M.R., Malappa, M., Murali Dhar, T., Cavallaro, C.L., Li, L., Oderinde, M.S., Smith, D., Pawluczyk, J.M., Kempson, J., Vetrichelvan, M., Gupta, A., Mathur, A., Rampulla, R., Weigelt, C.A., Lakkaraju, S.K., Khandelwal, P., Katepalli, M., Lenin, T.N.K., Riedmaier, S., DiPetrillo, K., Foster, K.A., Rayeni, M.K., Choure, V., Das, T., Levine, S., Kwok, M., Cvijic, M.E., Li, X., Fang, H., Tagore, D.M., Ravindran, M.S., Gujaran, S.R., Natarajan, A., Zhu, J., Pagarigan, B., Srinivas, P., Salinger, A., Dongre, A.R., Bell-Temin, H., Pham, H., Desai, P.R., Calder, O., Shi, L., Guo, S., Khambatta, G., Sivakumar, P., Ladygina, N., Narla, R.K., Dhar, G., Anandam, A., Khanna, V., Dudhgaonkar, S., Liu, J., Barnes, M.J., Borzilleri, R., Lombardo, L.J., Vite, G., Hunt, J.T., Balog, A.

(2026) J Med Chem

DOI: https://doi.org/10.1021/acs.jmedchem.6c01271

Macromolecule Content

Total Structure Weight: 148.71 kDa
Atom Count: 9,424
Modeled Residue Count: 1,209
Deposited Residue Count: 1,313
Unique protein chains: 3

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA damage-binding protein 1	A	856	Homo sapiens	Mutation(s): 0 Gene Names: DDB1, XAP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q16531 (Homo sapiens) Explore Q16531 Go to UniProtKB: Q16531
PHAROS: Q16531 GTEx: ENSG00000167986
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q16531
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein cereblon	B	426	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q96SW2
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Zinc finger protein Helios	C	31	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9UKS7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1CSO (Subject of Investigation/LOI) Query on A1CSO Download:Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	(3S)-3-[(3R,5M)-5-(6-amino-4,5-dimethylpyridin-2-yl)-4-fluoro-3-methyl-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione C₂₁ H₂₁ F N₄ O₃ CNRNDVOTRSDMEF-ABAIWWIYSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain F [auth C] SDF format, chain D [auth B] MOL2 format, chain F [auth C] MOL2 format, chain D [auth B] mmCIF format, chain F [auth C] mmCIF format, chain D [auth B]	D [auth B], F [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Focus chain F [auth C] Interactions & Density Focus chain D [auth B] Focus chain F [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.53 Å
R-Value Free: 0.236 (Depositor), 0.261 (DCC)
R-Value Work: 0.229 (Depositor), 0.249 (DCC)
R-Value Observed: 0.230 (Depositor)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 259.89	α = 90
b = 259.89	β = 90
c = 124.073	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
autoPROC	data scaling
XDS	data reduction
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-09-02

Deposition Author(s):

Pagarigan, B.E.

Funding Organization	Location	Grant Number
Other private		--

Revision History (Full details and data files)

Version 1.0: 2026-09-02
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.