2Z4B

Estrogen receptor beta ligand-binding domain complexed to a benzopyran ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.232 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Benzopyrans as selective estrogen receptor beta agonists (SERBAs). Part 3: Synthesis of cyclopentanone and cyclohexanone intermediates for C-ring modification.

Richardson, T.I.Dodge, J.A.Durst, G.L.Pfeifer, L.A.Shah, J.Wang, Y.Durbin, J.D.Krishnan, V.Norman, B.H.

(2007) Bioorg.Med.Chem.Lett. 17: 4824-4828

  • DOI: 10.1016/j.bmcl.2007.06.052
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Benzopyrans are selective estrogen receptor (ER) beta agonists (SERBAs), which bind the ER subtypes alpha and beta in opposite orientations. Here we describe the syntheses of cyclopentanone and cyclohexanone intermediates for SAR studies of the C-rin ...

    Benzopyrans are selective estrogen receptor (ER) beta agonists (SERBAs), which bind the ER subtypes alpha and beta in opposite orientations. Here we describe the syntheses of cyclopentanone and cyclohexanone intermediates for SAR studies of the C-ring on the benzopyran scaffold. Modification of the C-ring disrupts binding to ERalpha, thus improving ERbeta selectivity up to 100-fold. X-ray cocrystal structures confirm previously observed binding modes.


    Organizational Affiliation

    Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN 46285, USA. t_richardson@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
DC8
Query on DC8

Download SDF File 
Download CCD File 
A, B
(3AS,4R,9BR)-2,2-DIFLUORO-4-(4-HYDROXYPHENYL)-1,2,3,3A,4,9B-HEXAHYDROCYCLOPENTA[C]CHROMEN-8-OL
C18 H16 F2 O3
QJSMFUTULGSHNQ-ZOBUZTSGSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DC8Ki: 0.44 nM BINDINGMOAD
DC8Ki: 0.44 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.232 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 63.523α = 90.00
b = 63.523β = 90.00
c = 250.837γ = 120.00
Software Package:
Software NamePurpose
MAR345dtbdata collection
SCALAdata scaling
MOSFLMdata reduction
CNXrefinement
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2007-06-14 
  • Released Date: 2007-08-07 
  • Deposition Author(s): Wang, Y.

Revision History 

  • Version 1.0: 2007-08-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Derived calculations, Version format compliance