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

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.218 

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This is version 1.4 of the entry. See complete history


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

  • DOI: https://doi.org/10.1021/jm034243o
  • Primary Citation of Related Structures:  

  • 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.

  • Organizational Affiliation

    Department of Medicinal Chemistry, Atherosclerosis and Endocrinology, Merck Research Laboratories, P.O. Box 2000, 800-B109 Rahway, New Jersey 07065, USA. Seongkon_kim@merck.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Estrogen receptor248Homo sapiensMutation(s): 0 
Gene Names: ESR1NR3A1ESR
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03372
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on E4D

Download Ideal Coordinates CCD File 
C27 H29 N O4 S
Binding Affinity Annotations 
IDSourceBinding Affinity
E4D BindingDB:  1SJ0 IC50: min: 0.8, max: 9.6 (nM) from 3 assay(s)
PDBBind:  1SJ0 IC50: 0.8 (nM) from 1 assay(s)
Binding MOAD:  1SJ0 IC50: 0.8 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • 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 = 58.48α = 90
b = 58.48β = 90
c = 276.08γ = 120
Software Package:
Software NamePurpose
X-GENdata scaling
X-GENdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

  • 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