2POG

Benzopyrans as Selective Estrogen Receptor b Agonists (SERBAs). Part 2: Structure Activity Relationship Studies on the Benzopyran Scaffold.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.235 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Benzopyrans as selective estrogen receptor beta agonists (SERBAs). Part 2: structure-activity relationship studies on the benzopyran scaffold.

Richardson, T.I.Norman, B.H.Lugar, C.W.Jones, S.A.Wang, Y.Durbin, J.D.Krishnan, V.Dodge, J.A.

(2007) Bioorg Med Chem Lett 17: 3570-3574

  • DOI: https://doi.org/10.1016/j.bmcl.2007.04.051
  • Primary Citation of Related Structures:  
    2POG

  • 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 structure-activity relationship studies that led to the discovery of bezopyran 5b. X-ray crystal structures of 5b and a non-selective analog 5c in ERalpha help explain the observed selectivity of the benzopyran platform.


  • 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Estrogen receptor
A, B
248Homo sapiensMutation(s): 3 
Gene Names: ESR1
UniProt & NIH Common Fund Data Resources
Find proteins for P03372 (Homo sapiens)
Explore P03372 
Go to UniProtKB:  P03372
PHAROS:  P03372
GTEx:  ENSG00000091831 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03372
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
WST
Query on WST

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
(3AS,4R,9BR)-4-(4-HYDROXYPHENYL)-1,2,3,3A,4,9B-HEXAHYDROCYCLOPENTA[C]CHROMEN-9-OL
C18 H18 O3
FSYFYSFYUHBIHE-GLJUWKHASA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
WST PDBBind:  2POG Ki: 0.29 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.235 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.584α = 90
b = 99.81β = 90
c = 173.098γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
CNXphasing
CNXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-09-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-18
    Changes: Refinement description
  • Version 1.3: 2021-10-20
    Changes: Database references
  • Version 1.4: 2024-02-21
    Changes: Data collection