9B2B | pdb_00009b2b

Estrogen Receptor Alpha Ligand Binding Domain in Complex with a Complete Estrogen Receptor Antagonists that Favors Tetramer Formation

• PDB DOI: https://doi.org/10.2210/pdb9B2B/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-03-14 Released: 2025-08-27 
• Deposition Author(s): Fink, E.C., Chawla, R., Wells, K.S., Barratt, S., Myles, D.C., Pena, G., Robello, B.W., Ng, R., Fanning, S.W.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free: 
  0.318 (Depositor), 0.321 (DCC) 
• R-Value Work: 
  0.259 (Depositor), 0.264 (DCC) 
• R-Value Observed: 
  0.262 (Depositor) 

Starting Model: experimental

Literature

Allosteric Induction of Estrogen Receptor Ligand Binding Domain Tetramerization by a Distinct Complete Estrogen Receptor Antagonist.

Fink, E.C., Chawla, R., Hancock, G.R., Wells, K.S., Barratt, S., Myles, D.C., Pena, G., Robello, B.W., Hearn, B.R., Fanning, S.W.

(2026) ACS Med Chem Lett 17: 441-449

• PubMed: 41704390 
• DOI: https://doi.org/10.1021/acsmedchemlett.5c00667
• Primary Citation Related Structures: 
  9B2B


• PubMed Abstract: 
  

  Complete estrogen receptor antagonists (CERANs) are effective against advanced estrogen receptor-positive (ER+) breast cancers, but current chemical scaffolds limit our ability to explore the full range of ER pharmacology. We report the synthesis of OP-1690 ( 2 ), a CERAN featuring a distinct unconstrained core. Structural and biophysical studies reveal that 2 uniquely promotes estrogen receptor alpha (ERα) ligand binding domain (LBD) tetramer formation, which goes beyond the conventional homodimer. This study shows how new CERAN scaffolds can reveal unrecognized mechanisms of action.

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Organizational Affiliation: 
• Department of Cancer Biology, Loyola University Chicago Stritch School of Medicine, Maywood, Illinois 60546, United States.
Olema Oncology, San Francisco, California 94103, United States.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 118.3 kDa 
• Atom Count: 7,588 
• Modeled Residue Count: 895 
• Deposited Residue Count: 1,020 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Estrogen receptor	A, B, C, D	255	Homo sapiens	Mutation(s): 4  Gene Names: ESR1, ESR, NR3A1
UniProt & NIH Common Fund Data Resources
Find proteins for P03372 (Homo sapiens) Explore P03372  Go to UniProtKB:  P03372
PHAROS:  P03372 GTEx:  ENSG00000091831

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1AI0 (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth C], H [auth D]	2-chloro-3-{[{[1-(2-fluorophenyl)cyclopentyl]methyl}(4-{[1-(3-fluoropropyl)azetidin-3-yl]oxy}phenyl)amino]methyl}phenol C31 H35 Cl F2 N2 O2 IQQNTEIXXROPQR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free:  0.318 (Depositor), 0.321 (DCC) 
• R-Value Work:  0.259 (Depositor), 0.264 (DCC) 
• R-Value Observed: 0.262 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.097	α = 90
b = 57.419	β = 102.16
c = 174.803	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-08-27 
Deposition Author(s): Fink, E.C., Chawla, R., Wells, K.S., Barratt, S., Myles, D.C., Pena, G., Robello, B.W., Ng, R., Fanning, S.W.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	CA279341

Revision History  

• Version 1.0: 2025-08-27
  Type: Initial release
  
• Version 1.1: 2026-09-09
  Changes: Database references