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
  • Primary Citation of Related Structures:  

  • 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 BETA
A, B
257Homo sapiensMutation(s): 0 
Gene Names: ESR2 (ESTRB, NR3A2)
Find proteins for Q92731 (Homo sapiens)
Go to Gene View: ESR2
Go to UniProtKB:  Q92731
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JJ3
Query on JJ3

Download SDF File 
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 BINDINGMOAD
JJ3Ki: 0.28 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 = 90.00
b = 63.409β = 90.00
c = 248.907γ = 120.00
Software Package:
Software NamePurpose
CNXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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