2JJ3

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.235 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ESTROGEN RECEPTOR BETA
A, B
257Homo sapiensMutation(s): 0 
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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
JJ3
Query on JJ3

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
(3AS,4R,9BR)-4-(4-HYDROXYPHENYL)-6-(METHOXYMETHYL)-1,2,3,3A,4,9B-HEXAHYDROCYCLOPENTA[C]CHROMEN-8-OL
C20 H22 O4
RHQLNMNKTIOREN-AOIWGVFYSA-N
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)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
CNXrefinement
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
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references, Other