9ODR | pdb_00009odr

Structure of CRBN TBD bound to compound C1

PDB DOI: https://doi.org/10.2210/pdb9ODR/pdb

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

Deposited: 2025-04-27 Released: 2025-05-28
Deposition Author(s): Strickland, C., Rice, C.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.42 Å
R-Value Free:
0.228 (Depositor), 0.235 (DCC)
R-Value Work:
0.183 (Depositor), 0.188 (DCC)
R-Value Observed:
0.185 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Discovery and Characterization of PVTX-321 as a Potent and Orally Bioavailable Estrogen Receptor Degrader for ER+/HER2- Breast Cancer.

Xu, G., Havens, C.G., Deng, Q., Lowenstein, C., Samanta, D., Vidal, B., Behshad, E., Russell, M., Orth, P., Rice, C.T., Nagilla, R., Kirchhoff, P., Chen, Z., Rej, R.K., Acharyya, R.K., Wu, D., Wang, S., Zhang, W., Wu, W., Jolivette, L., Strickland, C., Sui, Z., Mohammad, H.P., Zhang, X., Priestley, E.S.

(2025) J Med Chem 68: 11299-11321

PubMed: 40366756 Search on PubMed
DOI: https://doi.org/10.1021/acs.jmedchem.5c00223
Primary Citation Related Structures:
9ODR, 9ODS

PubMed Abstract:
Estrogen receptor α (ERα) is a key therapeutic target in ER+/HER2- breast cancer, but ESR1 mutations drive resistance to endocrine therapies. Heterobifunctional degraders (HBDs) targeting ERα offer a promising strategy to overcome this resistance. Here, we report PVTX-321 ( 16a ), a potent ER HBD derived from a novel spirocyclic cereblon ligand and an ERα binder. PVTX-321 achieves a DC ₅₀ of 0.15 nM in MCF-7 cells and acts as a strong antagonist (IC ₅₀ = 59 nM), suppressing proliferation in ERα+ cell lines, including mutant variants (Y537S, D538G). It demonstrates favorable oral bioavailability, dose-dependent ERα degradation in vivo and induces tumor regression at 10 mg/kg (QD) in MCF-7 xenografts. With minimal CYP inhibition and a strong preclinical safety profile, PVTX-321 is a promising candidate for advancing ER+/HER2- breast cancer treatment.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 50.92 kDa
Atom Count: 3,537
Modeled Residue Count: 433
Deposited Residue Count: 444
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein cereblon	A, B, C, D	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q96SW2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1CAV (Subject of Investigation/LOI) Query on A1CAV Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain L [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain L [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain L [auth D]	E [auth A], G [auth B], I [auth C], L [auth D]	(3S)-3-(6-oxo-6,8-dihydro-2H,7H-spiro[furo[2,3-e]isoindole-3,4'-piperidin]-7-yl)piperidine-2,6-dione C₁₉ H₂₁ N₃ O₄ PMZFUWXTXQRRQU-AWEZNQCLSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain L [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain L [auth D]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain K [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain K [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain K [auth D]	F [auth A], H [auth B], J [auth C], K [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain K [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain K [auth D]