Crystal Structure of Estrogen Receptor beta complexed with CL-272

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.242 

wwPDB Validation   3D Report Full Report

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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

  • DOI: https://doi.org/10.1021/jm049719y
  • Primary Citation of Related Structures:  
    1U3Q, 1U3R, 1U3S

  • 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.

  • Organizational Affiliation

    Department of Chemical and Screening Sciences, Wyeth Research, CN 8000, Princeton, NJ 08543-8000, USA. malamam@wyeth.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Estrogen receptor beta
A, B, C, D
240Homo sapiensMutation(s): 0 
Gene Names: ESR2NR3A2ESTRB
UniProt & NIH Common Fund Data Resources
Find proteins for Q92731 (Homo sapiens)
Explore Q92731 
Go to UniProtKB:  Q92731
PHAROS:  Q92731
GTEx:  ENSG00000140009 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92731
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
272 BindingDB:  1U3Q IC50: 3.5 (nM) from 1 assay(s)
Binding MOAD:  1U3Q IC50: 3.5 (nM) from 1 assay(s)
PDBBind:  1U3Q IC50: 3.5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.242 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.167α = 90
b = 76.646β = 111.83
c = 82.8γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Entry History 

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations