Biological Assembly 1  

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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: 62792.27 
• Atom Count: 4133 
• Residue Count: 540 
• Unique protein chains: 2

1ZKY

Human Estrogen Receptor Alpha Ligand-Binding Domain In Complex With OBCP-3M and A Glucocorticoid Receptor Interacting Protein 1 Nr Box II Peptide

• DOI: 10.2210/pdb1ZKY/pdb

• Classification: HORMONE/GROWTH FACTOR RECEPTOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): 1 


• Deposited: 2005-05-04 Released: 2006-05-09 
• Deposition Author(s): Rajan, S.S., Hsieh, R.W., Sharma, S.K., Hahm, J.B., Nettles, K.W., Greene, G.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.231 
• R-Value Work: 0.185 

Literature

Identification of ligands with bicyclic scaffolds provides insights into mechanisms of estrogen receptor subtype selectivity.

Hsieh, R.W., Rajan, S.S., Sharma, S.K., Guo, Y., Desombre, E.R., Mrksich, M., Greene, G.L.

(2006) J.Biol.Chem. 281: 17909-17919

• PubMed: 16648639 
• DOI: 10.1074/jbc.M513684200
• Primary Citation of Related Structures:  
  2B1V, 2FAI
• Also Cited By: 2G44


• PubMed Abstract: 
  

Estrogen receptors alpha (ERalpha) and beta (ERbeta) have distinct functions and differential expression in certain tissues. These differences have stimulated the search for subtype-selective ligands. Therapeutically, such ligands offer the potential to target specific tissues or pathways regulated by one receptor subtype without affecting the other. As reagents, they can be utilized to probe the physiological functions of the ER subtypes to provide information complementary to that obtained from knock-out animals. A fluorescence resonance energy transfer-based assay was used to screen a 10,000-compound chemical library for ER agonists. From the screen, we identified a family of ERbeta-selective agonists whose members contain bulky oxabicyclic scaffolds in place of the planar scaffolds common to most ER ligands. These agonists are 10-50-fold selective for ERbeta in competitive binding assays and up to 60-fold selective in transactivation assays. The weak uterotrophic activity of these ligands in immature rats and their ability to stimulate expression of an ERbeta regulated gene in human U2OS osteosarcoma cells provides more physiological evidence of their ERbeta-selective nature. To provide insight into the molecular mechanisms of their activity and selectivity, we determined the crystal structures of the ERalpha ligand-binding domain (LBD) and a peptide from the glucocorticoid receptor-interacting protein 1 (GRIP1) coactivator complexed with the ligands OBCP-3M, OBCP-2M, and OBCP-1M. These structures illustrate how the bicyclic scaffolds of these ligands are accommodated in the flexible ligand-binding pocket of ER. A comparison of these structures with existing ER structures suggests that the ERbeta selectivity of OBCP ligands can be attributed to a combination of their interactions with Met-336 in ERbeta and Met-421 in ERalpha. These bicyclic ligands show promise as lead compounds that can target ERbeta. In addition, our understanding of the molecular determinants of their subtype selectivity provides a useful starting point for developing other ER modulators belonging to this relatively new structural class.

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Organizational Affiliation: 

Ben May Institute for Cancer Research, University of Chicago W330, 929 E. 57th Street, Chicago, IL 60637, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Estrogen receptor	A, B	257	Homo sapiens	Mutation(s): 1  Gene Names: ESR1 (ESR, NR3A1)
Find proteins for P03372 (Homo sapiens) Go to Gene View: ESR1 Go to UniProtKB:  P03372

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Nuclear receptor coactivator 2	C, D	13	Homo sapiens	Mutation(s): 0  Gene Names: NCOA2 (BHLHE75, SRC2, TIF2)
Find proteins for Q15596 (Homo sapiens) Go to Gene View: NCOA2 Go to UniProtKB:  Q15596

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
689	A, B	4-[(1S,2S,5S)-5-(HYDROXYMETHYL)-6,8,9-TRIMETHYL-3-OXABICYCLO[3.3.1]NON-7-EN-2-YL]PHENOL C18 H24 O3 DTZWKYVREFMAJA-QXWBOSQLSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME	A, B	L-PEPTIDE LINKING	C5 H11 N O3 S2		CYS

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
689	Ki: 560 nM BINDINGMOAD
689	Ki: 560 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.231 
• R-Value Work: 0.185 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 55.929	α = 90.00
b = 84.129	β = 109.06
c = 58.220	γ = 90.00

Software Package:

Software Name	Purpose
HKL-2000	data reduction
XTALVIEW	refinement
SCALEPACK	data scaling
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-05-04 
• Released Date: 2006-05-09 
• Deposition Author(s): Rajan, S.S., Hsieh, R.W., Sharma, S.K., Hahm, J.B., Nettles, K.W., Greene, G.L.

Revision History 

• Version 1.0: 2006-05-09
  Type: Initial release
• Version 1.1: 2008-04-30
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Advisory, Version format compliance