1ZAF

Crystal structure of estrogen receptor beta complexed with 3-Bromo-6-hydroxy-2-(4-hydroxy-phenyl)-inden-1-one

• PDB DOI: https://doi.org/10.2210/pdb1ZAF/pdb

• Classification: TRANSCRIPTION/TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-04-06 Released: 2006-04-11 
• Deposition Author(s): McDevitt, R.E., Malamas, M.S., Manas, E.S., Unwalla, R.J., Xu, Z.B., Miller, C.P., Harris, H.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.286 
• R-Value Work: 0.226 
• R-Value Observed: 0.226 

Literature

Estrogen receptor ligands: design and synthesis of new 2-arylindene-1-ones

McDevitt, R.E., Malamas, M.S., Manas, E.S., Unwalla, R.J., Xu, Z.B., Miller, C.P., Harris, H.A.

(2005) Bioorg Med Chem Lett 15: 3137-3142

• PubMed: 15876535 
• DOI: https://doi.org/10.1016/j.bmcl.2005.04.013
• Primary Citation of Related Structures:  
  1ZAF


• PubMed Abstract: 
  

  The syntheses of a series of 2-arylindene-1-ones as potent ligands of ERbeta and ERalpha are described. Several compounds exhibited high potency and moderate selectivity for the ERbeta receptor. X-ray and modeling studies were used to understand ligand binding orientation and observed affinity.

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Organizational Affiliation: 

Department of Chemical and Screening Sciences, Wyeth Research, CN 8000, Princeton, NJ 08543-8000, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

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

Macromolecule Content

• Total Structure Weight: 57.22 kDa 
• Atom Count: 4,001 
• Modelled Residue Count: 482 
• Deposited Residue Count: 502 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Estrogen receptor beta	A, B	238	Homo sapiens	Mutation(s): 0  Gene Names: ESR2, ESTRB, NR3A2
UniProt & NIH Common Fund Data Resources
Find proteins for Q92731 (Homo sapiens) Explore Q92731  Go to UniProtKB:  Q92731
PHAROS:  Q92731 GTEx:  ENSG00000140009

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor coactivator 1	C, D	13	N/A	Mutation(s): 0  EC: 2.3.1.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q15788 (Homo sapiens) Explore Q15788  Go to UniProtKB:  Q15788
PHAROS:  Q15788 GTEx:  ENSG00000084676

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
789	E [auth A], F [auth B]	3-BROMO-6-HYDROXY-2-(4-HYDROXYPHENYL)-1H-INDEN-1-ONE C15 H9 Br O3 DHPCBFMFERFZLR-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
789	BindingDB:  1ZAF	IC50: 20 (nM) from 1 assay(s)
	PDBBind:  1ZAF	IC50: 20 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.286 
• R-Value Work: 0.226 
• R-Value Observed: 0.226 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.281	α = 90
b = 89.213	β = 90
c = 99.334	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-04-11 
Deposition Author(s): McDevitt, R.E., Malamas, M.S., Manas, E.S., Unwalla, R.J., Xu, Z.B., Miller, C.P., Harris, H.A.

Revision History  

• Version 1.0: 2006-04-11
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations