1SJ0

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

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

  • DOI: 10.1021/jm034243o

  • 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 transactivatio ...

    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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Estrogen receptor
A
248Homo sapiensMutation(s): 0 
Gene Names: ESR1 (ESR, NR3A1)
Find proteins for P03372 (Homo sapiens)
Go to Gene View: ESR1
Go to UniProtKB:  P03372
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
E4D
Query on E4D

Download SDF File 
Download CCD File 
A
(2S,3R)-2-(4-(2-(PIPERIDIN-1-YL)ETHOXY)PHENYL)-2,3-DIHYDRO-3-(4-HYDROXYPHENYL)BENZO[B][1,4]OXATHIIN-6-OL
COMPOUND 4-D
C27 H29 N O4 S
TWZNCTCQAGRUGQ-RRPNLBNLSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
E4DIC50: 0.8 - 3.1 nM (100) BINDINGDB
E4DIC50: 0.8 nM BINDINGMOAD
E4DIC50: 0.8 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.218 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 58.480α = 90.00
b = 58.480β = 90.00
c = 276.080γ = 120.00
Software Package:
Software NamePurpose
X-GENdata scaling
SHELXLrefinement
X-GENdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-04-27
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description