2I0G

Benzopyrans are Selective Estrogen Receptor beta Agonists (SERBAs) with Novel Activity in Models of Benign Prostatic Hyperplasia


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.233 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Benzopyrans are selective estrogen receptor Beta agonists with novel activity in models of benign prostatic hyperplasia.

Norman, B.H.Dodge, J.A.Richardson, T.I.Borromeo, P.S.Lugar, C.W.Jones, S.A.Chen, K.Wang, Y.Durst, G.L.Barr, R.J.Montrose-Rafizadeh, C.Osborne, H.E.Amos, R.M.Guo, S.Boodhoo, A.Krishnan, V.

(2006) J.Med.Chem. 49: 6155-6157

  • DOI: 10.1021/jm060491j
  • Primary Citation of Related Structures:  2I0J

  • PubMed Abstract: 
  • Benzopyran selective estrogen receptor beta agonist-1 (SERBA-1) shows potent, selective binding and agonist function in estrogen receptor beta (ERbeta) in vitro assays. X-ray crystal structures of SERBA-1 in ERalpha and beta help explain observed bet ...

    Benzopyran selective estrogen receptor beta agonist-1 (SERBA-1) shows potent, selective binding and agonist function in estrogen receptor beta (ERbeta) in vitro assays. X-ray crystal structures of SERBA-1 in ERalpha and beta help explain observed beta-selectivity of this ligand. SERBA-1 in vivo demonstrates involution of the ventral prostate in CD-1 mice (ERbeta effect), while having no effect on gonadal hormone levels (ERalpha effect) at 10x the efficacious dose, consistent with in vitro properties of this molecule.


    Organizational Affiliation

    Discovery Chemistry Research, Bone and Inflammation Research, Lead Optimization Biology, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, USA. norman@lilly.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Estrogen receptor beta
A, B
257Homo sapiensGene 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
I0G
Query on I0G

Download SDF File 
Download CCD File 
A, B
(3AS,4R,9BR)-4-(4-HYDROXYPHENYL)-1,2,3,3A,4,9B-HEXAHYDROCYCLOPENTA[C]CHROMEN-8-OL
C18 H18 O3
XIESSJVMWNJCGZ-VKJFTORMSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
I0GEC50: 0.7 nM (100) BINDINGDB
I0GKi: 0.2 - 0.5 nM (100) BINDINGDB
I0GKi: 0.19 nM BINDINGMOAD
I0GKi: 0.19 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.233 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 63.196α = 90.00
b = 63.196β = 90.00
c = 249.255γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
ADSCdata collection
HKL-2000data reduction
AMoREphasing
CNXrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2006-08-10 
  • Released Date: 2006-10-24 
  • Deposition Author(s): Wang, Y.

Revision History 

  • Version 1.0: 2006-10-24
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description