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)

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
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Ligand Structure Quality Assessment

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Literature

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

Fanning, S.W.

To be published.

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P03372
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1AI0 (Subject of Investigation/LOI) Query on A1AI0 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth C] SDF format, chain H [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C] MOL2 format, chain H [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth C] mmCIF format, chain H [auth D]	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		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-08-27

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2025-08-27
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.