9ODR | pdb_00009odr

Structure of CRBN TBD bound to compound C1


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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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

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c00223
  • Primary Citation of 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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein cereblon
A, B, C, D
111Homo sapiensMutation(s): 0 
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
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1CAV (Subject of Investigation/LOI)
Query on A1CAV

Download Ideal Coordinates CCD File 
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
ZN
Query on ZN

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

Experimental Data

  • 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) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.35α = 90
b = 87.61β = 113.98
c = 89.5γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata scaling
XDSdata reduction
PDB_EXTRACTdata extraction
FFTphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-28
    Type: Initial release
  • Version 1.1: 2025-06-25
    Changes: Database references