1X7B

CRYSTAL STRUCTURE OF ESTROGEN RECEPTOR BETA COMPLEXED WITH ERB-041


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure-Based Design of Estrogen Receptor-Beta Selective Ligands

Manas, E.S.Unwalla, R.J.Xu, Z.B.Malamas, M.S.Miller, C.P.Harris, H.A.Hsiao, C.Akopian, T.Hum, W.T.Malakian, K.Wolfrom, S.Bapat, A.Bhat, R.A.Stahl, M.L.Somers, W.S.Alvarez, J.C.

(2004) J.Am.Chem.Soc. 126: 15106-15119

  • DOI: 10.1021/ja047633o
  • Primary Citation of Related Structures:  1U9E, 1X76, 1X78, 1X7E

  • PubMed Abstract: 
  • We present the structure-based optimization of a series of estrogen receptor-beta (ERbeta) selective ligands. X-ray cocrystal structures of these ligands complexed to both ERalpha and ERbeta are described. We also discuss how molecular modeling was u ...

    We present the structure-based optimization of a series of estrogen receptor-beta (ERbeta) selective ligands. X-ray cocrystal structures of these ligands complexed to both ERalpha and ERbeta are described. We also discuss how molecular modeling was used to take advantage of subtle differences between the two binding cavities in order to optimize selectivity for ERbeta over ERalpha. Quantum chemical calculations are utilized to gain insight into the mechanism of selectivity enhancement. Despite only two relatively conservative residue substitutions in the ligand binding pocket, the most selective compounds have greater than 100-fold selectivity for ERbeta relative to ERalpha when measured using a competitive radioligand binding assay.


    Organizational Affiliation

    Department of Chemical and Screening Sciences, Wyeth Research, 500 Arcola Road, Collegeville, Pennsylvania 19426, USA. manase@wyeth.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Estrogen receptor beta
A, B
240Homo sapiensGene 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
13N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
041
Query on 041

Download SDF File 
Download CCD File 
A, B
2-(3-FLUORO-4-HYDROXYPHENYL)-7-VINYL-1,3-BENZOXAZOL-5-OL
C15 H10 F N O3
MQIMZDXIAHJKQP-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
041IC50: 3.1 - 5 nM (92) BINDINGDB
041IC50: 4.1 nM BINDINGMOAD
41IC50: 4.1 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.218 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 52.181α = 90.00
b = 87.981β = 90.00
c = 99.918γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
HKL-2000data collection
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-03-01
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance