Benzopyrans are Selective Estrogen Receptor beta Agonists (SERBAs) with Novel Activity in Models of Benign Prostatic Hyperplasia

Experimental Data Snapshot

  • Resolution: 2.90 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.242 

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Benzopyrans are selective estrogen receptor Beta agonists with novel activity in models of benign prostatic hyperplasia.

Norman, B.H.Dodge, J.A.Richardson, T.I.Borromeo, P.S.Lugar, C.W.Jones, S.A.Chen, K.Wang, Y.Durst, G.L.Barr, R.J.Montrose-Rafizadeh, C.Osborne, H.E.Amos, R.M.Guo, S.Boodhoo, A.Krishnan, V.

(2006) J Med Chem 49: 6155-6157

  • DOI: https://doi.org/10.1021/jm060491j
  • Primary Citation of Related Structures:  
    2I0G, 2I0J

  • PubMed Abstract: 

    Benzopyran selective estrogen receptor beta agonist-1 (SERBA-1) shows potent, selective binding and agonist function in estrogen receptor beta (ERbeta) in vitro assays. X-ray crystal structures of SERBA-1 in ERalpha and beta help explain observed beta-selectivity of this ligand. SERBA-1 in vivo demonstrates involution of the ventral prostate in CD-1 mice (ERbeta effect), while having no effect on gonadal hormone levels (ERalpha effect) at 10x the efficacious dose, consistent with in vitro properties of this molecule.

  • Organizational Affiliation

    Discovery Chemistry Research, Bone and Inflammation Research, Lead Optimization Biology, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, USA. norman@lilly.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Estrogen receptor alpha
A, B, C, D
244Homo sapiensMutation(s): 3 
Gene Names: ESR1ESRNR3A1
UniProt & NIH Common Fund Data Resources
Find proteins for P03372 (Homo sapiens)
Explore P03372 
Go to UniProtKB:  P03372
PHAROS:  P03372
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03372
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
I0G BindingDB:  2I0J Ki: min: 2.29, max: 4.34 (nM) from 4 assay(s)
EC50: 19.4 (nM) from 1 assay(s)
PDBBind:  2I0J Ki: 2.68 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.90 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.242 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.503α = 90
b = 173.144β = 119.48
c = 58.522γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
MAR345data collection
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

  • Released Date: 2006-10-24 
  • Deposition Author(s): Wang, Y.

Revision History  (Full details and data files)

  • Version 1.0: 2006-10-24
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.5: 2023-08-30
    Changes: Data collection, Refinement description