2R6Y

Estrogen receptor alpha ligand-binding domain in complex with a SERM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Prediction of the tissue-specificity of selective estrogen receptor modulators by using a single biochemical method.

Dai, S.Y.Chalmers, M.J.Bruning, J.Bramlett, K.S.Osborne, H.E.Montrose-Rafizadeh, C.Barr, R.J.Wang, Y.Wang, M.Burris, T.P.Dodge, J.A.Griffin, P.R.

(2008) Proc.Natl.Acad.Sci.Usa 105: 7171-7176

  • DOI: 10.1073/pnas.0710802105
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Here, we demonstrate that a single biochemical assay is able to predict the tissue-selective pharmacology of an array of selective estrogen receptor modulators (SERMs). We describe an approach to classify estrogen receptor (ER) modulators based on dy ...

    Here, we demonstrate that a single biochemical assay is able to predict the tissue-selective pharmacology of an array of selective estrogen receptor modulators (SERMs). We describe an approach to classify estrogen receptor (ER) modulators based on dynamics of the receptor-ligand complex as probed with hydrogen/deuterium exchange (HDX) mass spectrometry. Differential HDX mapping coupled with cluster and discriminate analysis effectively predicted tissue-selective function in most, but not all, cases tested. We demonstrate that analysis of dynamics of the receptor-ligand complex facilitates binning of ER modulators into distinct groups based on structural dynamics. Importantly, we were able to differentiate small structural changes within ER ligands of the same chemotype. In addition, HDX revealed differentially stabilized regions within the ligand-binding pocket that may contribute to the different pharmacology phenotypes of the compounds independent of helix 12 positioning. In summary, HDX provides a sensitive and rapid approach to classify modulators of the estrogen receptor that correlates with their pharmacological profile.


    Organizational Affiliation

    Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, FL 33458, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Estrogen receptor
A, B
248Homo sapiensMutation(s): 3 
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
LLC
Query on LLC

Download SDF File 
Download CCD File 
A, B
[6-hydroxy-2-(4-hydroxyphenyl)-1-benzothien-3-yl][4-(2-pyrrolidin-1-ylethoxy)phenyl]methanone
C27 H25 N O4 S
JLERVPBPJHKRBJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
LLCKi: 0.32 nM BINDINGMOAD
LLCKi: 0.32 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.210 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 63.132α = 90.00
b = 98.737β = 90.00
c = 174.981γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
MAR345dtbdata collection
AMoREphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2007-09-06 
  • Released Date: 2008-04-08 
  • Deposition Author(s): Wang, Y.

Revision History 

  • Version 1.0: 2008-04-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance