Biological Assembly 1  

 3D View: Structure | 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: 57.86 kDa 
• Atom Count: 3935 
• Residue Count: 476 
• Unique protein chains: 2

1U3R

Crystal Structure of Estrogen Receptor beta complexed with WAY-338

• DOI: 10.2210/pdb1U3R/pdb

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


• Deposited: 2004-07-22 Released: 2005-07-26 
• Deposition Author(s): Malamas, M.S., Manas, E.S., McDevitt, R.E., Gunawan, I., Xu, Z.B., Collini, M.D., Miller, C.P., Dinh, T., Henderson, R.A., Keith Jr., J.C., Harris, H.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free: 0.267 
• R-Value Work: 0.218 
• R-Value Observed: 0.220 

Literature

Design and synthesis of aryl diphenolic azoles as potent and selective estrogen receptor-beta ligands.

Malamas, M.S., Manas, E.S., McDevitt, R.E., Gunawan, I., Xu, Z.B., Collini, M.D., Miller, C.P., Dinh, T., Henderson, R.A., Keith Jr., J.C., Harris, H.A.

(2004) J Med Chem 47: 5021-5040

• PubMed: 15456246 
• DOI: 10.1021/jm049719y
• Primary Citation of Related Structures:  
  1U3S, 1U3R, 1U3Q


• PubMed Abstract: 
  

New diphenolic azoles as highly selective estrogen receptor-beta agonists are reported. The more potent and selective analogues of these series have comparable binding affinities for ERbeta as the natural ligand 17beta-estradiol but are >100-fold selective over ERalpha. Our design strategy not only followed a traditional SAR approach but also was supported by X-ray structures of ERbeta cocrystallized with various ligands as well as molecular modeling studies. These strategies enabled us to take advantage of a single conservative residue substitution in the ligand-binding pocket, ERalpha Met(421) --> ERbeta Ile(373), to optimize ERbeta selectivity. The 7-position-substituted benzoxazoles (Table 5) were the most selective ligands of both azole series, with ERB-041 (117) being >200-fold selective for ERbeta. The majority of ERbeta selective agonists tested that were at least approximately 50-fold selective displayed a consistent in vivo profile: they were inactive in several models of classic estrogen action (uterotrophic, osteopenia, and vasomotor instability models) and yet were active in the HLA-B27 transgenic rat model of inflammatory bowel disease. These data suggest that ERbeta-selective agonists are devoid of classic estrogenic effects and may offer a novel therapy to treat certain inflammatory conditions.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Estrogen receptor beta	A, B	241	Homo sapiens	Mutation(s): 0  Gene Names: ESR2, NR3A2, ESTRB
Find proteins for Q92731 (Homo sapiens) Explore Q92731  Go to UniProtKB:  Q92731
NIH Common Fund Data Resources
PHAROS  Q92731 GTEx  ENSG00000140009

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
338	A, B	2-(5-HYDROXY-NAPHTHALEN-1-YL)-1,3-BENZOOXAZOL-6-OL C17 H11 N O3 JHOZVRGNIYFYHE-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
338	IC50 :  5   nM  PDBBind
338	IC50:  5   nM  Binding MOAD
338	IC50:  5   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free: 0.267 
• R-Value Work: 0.218 
• R-Value Observed: 0.220 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.154	α = 90
b = 87.884	β = 90
c = 99.432	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-07-22 
• Released Date: 2005-07-26 
Deposition Author(s): Malamas, M.S., Manas, E.S., McDevitt, R.E., Gunawan, I., Xu, Z.B., Collini, M.D., Miller, C.P., Dinh, T., Henderson, R.A., Keith Jr., J.C., Harris, H.A.

Revision History 

• Version 1.0: 2005-07-26
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance