1X7R

CRYSTAL STRUCTURE OF ESTROGEN RECEPTOR ALPHA COMPLEXED WITH GENISTEIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.225 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Understanding the Selectivity of Genistein for Human Estrogen Receptor-Beta Using X-Ray Crystallography and Computational Methods

Manas, E.S.Xu, Z.B.Unwalla, R.J.Somers, W.S.

(2004) Structure 12: 2197-2207

  • DOI: 10.1016/j.str.2004.09.015
  • Primary Citation of Related Structures:  
    1X7J, 1X7R

  • PubMed Abstract: 
  • We present X-ray crystallographic and molecular modeling studies of estrogen receptors-alpha and -beta complexed with the estrogen receptor-beta-selective phytoestrogen genistein, and coactivator-derived NR box peptides containing an LXXLL motif. We demonstrate that the ligand binding mode is essentially identical when genistein is bound to both isoforms, despite the considerably weaker affinity of this ligand for estrogen receptor-alpha ...

    We present X-ray crystallographic and molecular modeling studies of estrogen receptors-alpha and -beta complexed with the estrogen receptor-beta-selective phytoestrogen genistein, and coactivator-derived NR box peptides containing an LXXLL motif. We demonstrate that the ligand binding mode is essentially identical when genistein is bound to both isoforms, despite the considerably weaker affinity of this ligand for estrogen receptor-alpha. In addition, we examine subtle differences between binding site residues, providing an explanation for why genistein is modestly selective for the beta isoform. To this end, we also present the results of quantum chemical studies and thermodynamic arguments that yield insight to the nature of the interactions leading to estrogen receptor-beta selectivity. The importance of our analysis to structure-based drug design is discussed.


    Organizational Affiliation

    Department of Chemical and Screening Sciences, Wyeth Research, 500 Arcola Road, Collegeville, PA 19426, USA. manase@wyeth.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Estrogen receptor 1 (alpha)A245Homo 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
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
steroid receptor coactivator-3B13N/AMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GEN (Subject of Investigation/LOI)
Query on GEN

Download Ideal Coordinates CCD File 
C [auth A]GENISTEIN
C15 H10 O5
TZBJGXHYKVUXJN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GENIC50:  580   nM  BindingDB
GENIC50:  2150   nM  BindingDB
GENIC50:  1973   nM  BindingDB
GENIC50 :  9   nM  PDBBind
GENIC50:  9.699999809265137   nM  BindingDB
GENIC50:  395   nM  BindingDB
GENIC50:  6100   nM  BindingDB
GENIC50:  92   nM  BindingDB
GENIC50:  1300   nM  BindingDB
GENKi:  370   nM  BindingDB
GENEC50:  810   nM  BindingDB
GENIC50:  360   nM  Binding MOAD
GENIC50:  300   nM  BindingDB
GENIC50:  4660   nM  BindingDB
GENIC50:  4680   nM  BindingDB
GENEC50:  48   nM  BindingDB
GENIC50:  1145   nM  BindingDB
GENEC50:  240   nM  BindingDB
GENEC50:  950   nM  BindingDB
GENEC50:  956   nM  BindingDB
GENIC50:  990   nM  BindingDB
GENIC50:  3920   nM  BindingDB
GENEC50:  20   nM  BindingDB
GENIC50:  29.399999618530273   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.225 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.882α = 90
b = 69.833β = 90
c = 57.365γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-03-01
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance