1SJ0

Human Estrogen Receptor Alpha Ligand-binding Domain in Complex with the Antagonist Ligand 4-D

• PDB DOI: https://doi.org/10.2210/pdb1SJ0/pdb

• Classification: HORMONE/GROWTH FACTOR RECEPTOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-03-02 Released: 2004-04-27 
• Deposition Author(s): Kim, S., Wu, J.Y., Birzin, E.T., Chan, W., Pai, L.Y., Yang, Y.T., Mosley, R.T., Fitzgerald, P.M., Sharma, N., DiNinno, F., Rohrer, S.P., Schaeffer, J.M., Hammond, M.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.272 
• R-Value Work: 0.218 
• R-Value Observed: 0.218 

Literature

Estrogen Receptor Ligands. II. Discovery of Benzoxathiins as Potent, Selective Estrogen Receptor alpha Modulators.

Kim, S., Wu, J.Y., Birzin, E.T., Frisch, K., Chan, W., Pai, L.Y., Yang, Y.T., Mosley, R.T., Fitzgerald, P.M., Sharma, N., Dahllund, J., Thorsell, A.G., DiNinno, F., Rohrer, S.P., Schaeffer, J.M., Hammond, M.L.

(2004) J Med Chem 47: 2171-2175

• PubMed: 15084115 
• DOI: https://doi.org/10.1021/jm034243o
• Primary Citation of Related Structures:  
  1SJ0


• PubMed Abstract: 
  

  The discovery and synthesis of dihydrobenzoxathiins as potent, ERalpha subtype selective ligands are described. The most active analogue, 4-D, was found to be 50-fold selective in a competitive binding assay and 100-fold selective in a transactivation assay in HEK-293 cells. The alpha selectivity was postulated to lie in the interaction of the sulfur atom of the benzoxathiin ring with the two discriminating residues in the binding pocket of the receptor isoforms.

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Organizational Affiliation: 

Department of Medicinal Chemistry, Atherosclerosis and Endocrinology, Merck Research Laboratories, P.O. Box 2000, 800-B109 Rahway, New Jersey 07065, USA. [e-mail]

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,PQS (software)

Macromolecule Content

• Total Structure Weight: 28.78 kDa 
• Atom Count: 2,119 
• Modelled Residue Count: 243 
• Deposited Residue Count: 248 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Estrogen receptor	A	248	Homo sapiens	Mutation(s): 0  Gene Names: ESR1, NR3A1, ESR
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
E4D	B [auth A]	(2S,3R)-2-(4-(2-(PIPERIDIN-1-YL)ETHOXY)PHENYL)-2,3-DIHYDRO-3-(4-HYDROXYPHENYL)BENZO[B][1,4]OXATHIIN-6-OL C27 H29 N O4 S TWZNCTCQAGRUGQ-RRPNLBNLSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
E4D	PDBBind:  1SJ0	IC50: 0.8 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.272 
• R-Value Work: 0.218 
• R-Value Observed: 0.218 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.48	α = 90
b = 58.48	β = 90
c = 276.08	γ = 120

Software Package:

Software Name	Purpose
X-GEN	data scaling
X-GEN	data reduction
SHELXL	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-04-27 
Deposition Author(s): Kim, S., Wu, J.Y., Birzin, E.T., Chan, W., Pai, L.Y., Yang, Y.T., Mosley, R.T., Fitzgerald, P.M., Sharma, N., DiNinno, F., Rohrer, S.P., Schaeffer, J.M., Hammond, M.L.

Revision History  

• Version 1.0: 2004-04-27
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references, Derived calculations