1YY4

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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

  • DOI: 10.1021/jm058173s
  • Primary Citation of Related Structures:  

  • 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 pot ...

    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.


    Organizational Affiliation

    Chemical and Screening Sciences, Wyeth Research, Collegeville, Pennsylvania 19426, USA. mewshar@wyeth.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Estrogen receptor beta
A, B
268Homo sapiensMutation(s): 0 
Gene Names: ESR2 (ESTRB, NR3A2)
Find proteins for Q92731 (Homo sapiens)
Go to Gene View: ESR2
Go to UniProtKB:  Q92731
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
STEROID RECEPTOR COACTIVATOR-1
C, D
13Homo sapiensMutation(s): 0 
Gene Names: NCOA1 (BHLHE74, SRC1)
EC: 2.3.1.48
Find proteins for Q15788 (Homo sapiens)
Go to Gene View: NCOA1
Go to UniProtKB:  Q15788
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4NA
Query on 4NA

Download SDF File 
Download CCD File 
A, B
1-CHLORO-6-(4-HYDROXYPHENYL)-2-NAPHTHOL
C16 H11 Cl O2
YHEHVRSGKUYDON-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
4NAIC50: 2.52 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.214 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 51.970α = 90.00
b = 87.677β = 90.00
c = 99.760γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
AMoREphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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