Estrogen receptor beta ligand binding domain in complex with a Benzopyran agonist

Experimental Data Snapshot

  • Resolution: 2.28 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.235 

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This is version 1.2 of the entry. See complete history


Benzopyrans as Selective Estrogen Receptor Beta Agonists (Serbas). Part 4: Functionalization of the Benzopyran A-Ring.

Norman, B.H.Richardson, T.I.Dodge, J.A.Pfeifer, L.A.Durst, G.L.Wang, Y.Durbin, J.D.Krishnan, V.Dinn, S.R.Liu, S.Reilly, J.E.Ryter, K.T.

(2007) Bioorg Med Chem Lett 17: 5082

  • DOI: https://doi.org/10.1016/j.bmcl.2007.07.009
  • Primary Citation of Related Structures:  
    2JJ3, 2QE4

  • PubMed Abstract: 

    Benzopyrans are selective estrogen receptor (ER) beta agonists (SERBAs), which bind the ER receptor subtypes alpha and beta in opposite orientations. We have used structure based drug design to show that this unique phenomena can be exploited via substitution at the 8-position of the benzopyran A-ring to disrupt binding to ERalpha, thus improving ERbeta subtype selectivity. X-ray cocrystal structures with ERalpha and ERbeta are supportive of this approach to improve selectivity in this structural class.

  • Organizational Affiliation

    Discovery Chemistry Research, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN 46285, USA. norman@lilly.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
257Homo sapiensMutation(s): 0 
Gene Names: ESR2ESTRBNR3A2
UniProt & NIH Common Fund Data Resources
Find proteins for Q92731 (Homo sapiens)
Explore Q92731 
Go to UniProtKB:  Q92731
PHAROS:  Q92731
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92731
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on JJ3

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C20 H22 O4
Binding Affinity Annotations 
IDSourceBinding Affinity
JJ3 PDBBind:  2JJ3 Ki: 0.28 (nM) from 1 assay(s)
BindingDB:  2JJ3 Ki: 0.28 (nM) from 1 assay(s)
Binding MOAD:  2JJ3 Ki: 0.28 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.28 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.235 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.409α = 90
b = 63.409β = 90
c = 248.907γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2007-08-07
    Type: Initial release
  • Version 1.1: 2011-05-07
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance