2QE4

Estrogen receptor alpha ligand-binding domain in complex with a benzopyran agonist


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.241 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Benzopyrans as selective estrogen receptor beta agonists (SERBAs). Part 4: Functionalization of the benzopyran A-ring.

Norman, B.H.Richardson, T.I.Dodge, J.A.Pfeifer, L.A.Durst, G.L.Wang, Y.Durbin, J.D.Krishnan, V.Dinn, S.R.Liu, S.Reilly, J.E.Ryter, K.T.

(2007) Bioorg Med Chem Lett 17: 5082-5085

  • DOI: 10.1016/j.bmcl.2007.07.009
  • Primary Citation of Related Structures:  
    2JJ3, 2QE4

  • PubMed Abstract: 
  • Benzopyrans are selective estrogen receptor (ER) beta agonists (SERBAs), which bind the ER receptor subtypes alpha and beta in opposite orientations. We have used structure based drug design to show that this unique phenomena can be exploited via substitution at the 8-position of the benzopyran A-ring to disrupt binding to ERalpha, thus improving ERbeta subtype selectivity ...

    Benzopyrans are selective estrogen receptor (ER) beta agonists (SERBAs), which bind the ER receptor subtypes alpha and beta in opposite orientations. We have used structure based drug design to show that this unique phenomena can be exploited via substitution at the 8-position of the benzopyran A-ring to disrupt binding to ERalpha, thus improving ERbeta subtype selectivity. X-ray cocrystal structures with ERalpha and ERbeta are supportive of this approach to improve selectivity in this structural class.


    Organizational Affiliation

    Discovery Chemistry Research, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN 46285, USA. norman@lilly.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Estrogen receptorA, B248Homo sapiensMutation(s): 3 
Gene Names: ESR1ESRNR3A1
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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JJ3
Query on JJ3

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
(3AS,4R,9BR)-4-(4-HYDROXYPHENYL)-6-(METHOXYMETHYL)-1,2,3,3A,4,9B-HEXAHYDROCYCLOPENTA[C]CHROMEN-8-OL
C20 H22 O4
RHQLNMNKTIOREN-AOIWGVFYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
JJ3 PDBBind:  2QE4 Ki: 11 (nM) from 1 assay(s)
BindingDB:  2QE4 Ki: min: 11, max: 11.9 (nM) from 2 assay(s)
Binding MOAD:  2QE4 Ki: 11 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.241 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.915α = 90
b = 54.091β = 91.24
c = 84.169γ = 90
Software Package:
Software NamePurpose
CNXrefinement
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-09-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-10-20
    Changes: Database references