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 

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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: https://doi.org/10.1016/j.bmcl.2007.06.052
  • Primary Citation of Related Structures:  
    2Q70, 2Z4B

  • 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-ring on the benzopyran scaffold ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Estrogen receptor beta
A, B
257Homo sapiensMutation(s): 0 
Gene Names: ESR2, ESTRB, NR3A2
UniProt & NIH Common Fund Data Resources
Find proteins for Q92731 (Homo sapiens)
Explore Q92731 
Go to UniProtKB:  Q92731
PHAROS:  Q92731
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92731
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DC8
Query on DC8
Download Ideal Coordinates CCD File 
C [auth A],
D [auth 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
Binding Affinity Annotations 
IDSourceBinding Affinity
DC8 PDBBind:  2Z4B Ki: 0.44 (nM) from 1 assay(s)
Binding MOAD:  2Z4B Ki: 0.44 (nM) from 1 assay(s)
BindingDB:  2Z4B Ki: 0.44 (nM) from 1 assay(s)
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

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Entry History 

Deposition Data

  • Released Date: 2007-08-07 
    • Deposition Author(s): Wang, Y.

Revision History  (Full details and data files)

  • Version 1.0: 2007-08-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Derived calculations, Version format compliance