Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 57.57 kDa 
• Atom Count: 3799 
• Modelled Residue Count: 452 
• Deposited Residue Count: 496 
• Unique protein chains: 1

2R6W

Estrogen receptor alpha ligand-binding domain complexed to a SERM

• DOI: 10.2210/pdb2R6W/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.257 
• R-Value Work: 0.208 
• R-Value Observed: 0.212 

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

• PubMed: 18474858 
• DOI: 10.1073/pnas.0710802105
• Primary Citation of Related Structures:  
  2R6Y, 2R6W


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Estrogen receptor	A, B	248	Homo sapiens	Mutation(s): 3  Gene Names: ESR1, ESR, NR3A1
Find proteins for P03372 (Homo sapiens) Explore P03372  Go to UniProtKB:  P03372
NIH Common Fund Data Resources
PHAROS:  P03372 GTEx:  ENSG00000091831

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LLB	A, B	[6-hydroxy-2-(4-hydroxyphenyl)-1-benzothien-3-yl]{4-[2-(4-methylpiperidin-1-yl)ethoxy]phenyl}methanone C29 H29 N O4 S RLOZWABDAGQFIY-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
LLB	Ki :  0.4399999976158142   nM  PDBBind
LLB	Ki:  0.4399999976158142   nM  Binding MOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.257 
• R-Value Work: 0.208 
• R-Value Observed: 0.212 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.47	α = 90
b = 102.761	β = 90
c = 172.952	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345dtb	data collection
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing

Structure Validation

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