Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | 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: 63.36 kDa 
• Atom Count: 3866 
• Modelled Residue Count: 468 
• Deposited Residue Count: 562 
• Unique protein chains: 2

1YY4

Crystal structure of estrogen receptor beta complexed with 1-chloro-6-(4-hydroxy-phenyl)-naphthalen-2-ol

• PDB DOI: 10.2210/pdb1YY4/pdb

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


• Deposited: 2005-02-23 Released: 2006-02-28 
• Deposition Author(s): Mewshaw, R.E., Edsall Jr., R.J., Yang, C., Manas, E.S., Xu, Z.B., Henderson, R.A., Keith Jr., J.C., Harris, H.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.269 
• R-Value Work: 0.214 
• R-Value Observed: 0.217 

Literature

ERbeta ligands. 3. Exploiting two binding orientations of the 2-phenylnaphthalene scaffold to achieve ERbeta selectivity

Mewshaw, R.E., Edsall Jr., R.J., Yang, C., Manas, E.S., Xu, Z.B., Henderson, R.A., Keith Jr., J.C., Harris, H.A.

(2005) J Med Chem 48: 3953-3979

• PubMed: 15943471 
• DOI: 10.1021/jm058173s
• Primary Citation of Related Structures:  
  1YY4, 1YYE


• PubMed Abstract: 
  

The 2-phenylnaphthalene scaffold was explored as a simplified version of genistein in order to identify ER selective ligands. With the aid of docking studies, positions 1, 4, and 8 of the 2-phenylnaphthalene template were predicted to be the most potentially influential positions to enhance ER selectivity using two different binding orientations. Both orientations have the phenol moiety mimicking the A-ring of genistein. Several compounds predicted to adopt orientations similar to that of genistein when bound to ERbeta were observed to have slightly higher ER affinity and selectivity than genistein. The second orientation we exploited, which was different from that of genistein when bound to ERbeta, resulted in the discovery of several compounds that had superior ER selectivity and affinity versus genistein. X-ray structures of two ER selective compounds (i.e., 15 and 47) confirmed the alternate binding mode and suggested that substituents at positions 1 and 8 were responsible for inducing selectivity. One compound (i.e., 47, WAY-202196) was further examined and found to be effective in two models of inflammation, suggesting that targeting ER may be therapeutically useful in treating certain chronic inflammatory diseases.

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Organizational Affiliation: 

Chemical and Screening Sciences, Wyeth Research, Collegeville, Pennsylvania 19426, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Estrogen receptor beta	A, B	268	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

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4NA	E [auth A], F [auth B]	1-CHLORO-6-(4-HYDROXYPHENYL)-2-NAPHTHOL C16 H11 Cl O2 YHEHVRSGKUYDON-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
4NA	PDBBind:  1YY4	IC50: 2.52 (nM) from 1 assay(s)
	BindingDB:  1YY4	IC50: 2.52 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.269 
• R-Value Work: 0.214 
• R-Value Observed: 0.217 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.97	α = 90
b = 87.677	β = 90
c = 99.76	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-02-23 
• Released Date: 2006-02-28 
Deposition Author(s): Mewshaw, R.E., Edsall Jr., R.J., Yang, C., Manas, E.S., Xu, Z.B., Henderson, R.A., Keith Jr., J.C., Harris, H.A.

Revision History  

• Version 1.0: 2006-02-28
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance