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


This is version 1.2 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: 10.1016/j.bmcl.2007.07.009
  • Structures With Same Primary Citation

  • 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 sub ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ESTROGEN RECEPTOR BETAA, B257Homo sapiensMutation(s): 0 
Gene Names: ESR2ESTRBNR3A2
Find proteins for Q92731 (Homo sapiens)
Explore Q92731 
Go to UniProtKB:  Q92731
NIH Common Fund Data Resources
PHAROS  Q92731
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JJ3
Query on JJ3

Download CCD File 
A, 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
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
JJ3Kd:  281   nM  Binding MOAD
JJ3Ki:  0.2800000011920929   nM  BindingDB
JJ3Ki :  0.2800000011920929   nM  PDBBind
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

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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