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
  • Structures With Same Primary Citation

  • 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 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
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DC8
Query on DC8

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 :  0.4399999976158142   nM  PDBBind
DC8Ki:  0.4399999976158142   nM  BindingDB
DC8Ki:  0.4399999976158142   nM  Binding MOAD
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
b = 63.523β = 90
c = 250.837γ = 120
Software Package:
Software NamePurpose
CNXrefinement
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



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
    Changes: Derived calculations, Version format compliance