2R6Y

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 

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 U S A 105: 7171-7176

  • DOI: 10.1073/pnas.0710802105
  • Structures With Same Primary Citation

  • 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: ESR1ESRNR3A1
Find proteins for P03372 (Homo sapiens)
Go to UniProtKB:  P03372
NIH Common Fund Data Resources
PHAROS  P03372
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LLC
Query on LLC

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:  0.3199999928474426   nM  Binding MOAD
LLCKi :  0.3199999928474426   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.132α = 90
b = 98.737β = 90
c = 174.981γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing

Structure Validation

View Full Validation Report



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
    Changes: Version format compliance