2Q70

Estrogen receptor alpha ligand-binding domain complxed to a benzopyran ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.260 

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
A, B
248Homo sapiensMutation(s): 3 
Gene Names: ESR1ESRNR3A1
Find proteins for P03372 (Homo sapiens)
Go to UniProtKB:  P03372
NIH Common Fund Data Resources
PHAROS  P03372
Protein Feature View
  • 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:  8.399999618530273   nM  BindingDB
DC8Ki:  8.300000190734863   nM  Binding MOAD
DC8Ki:  8.300000190734863   nM  BindingDB
DC8Ki :  8.300000190734863   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.260 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.558α = 90
b = 97.88β = 90
c = 174.156γ = 90
Software Package:
Software NamePurpose
CNXrefinement
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
CNXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2007-06-05 
  • 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: Version format compliance