2Z4B | pdb_00002z4b

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 (Depositor), 0.251 (DCC) 
  • R-Value Work: 
    0.232 (Depositor), 0.231 (DCC) 

wwPDB Validation 3D Report Full Report

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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 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 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. 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

Macromolecule Content 

  • Total Structure Weight: 59.09 kDa 
  • Atom Count: 3,595 
  • Modeled Residue Count: 445 
  • Deposited Residue Count: 514 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Estrogen receptor beta
A, B
257Homo sapiensMutation(s): 0 
Gene Names: ESR2
UniProt & NIH Common Fund Data Resources
Find proteins for Q92731 (Homo sapiens)
Explore Q92731 
Go to UniProtKB:  Q92731
PHAROS:  Q92731
GTEx:  ENSG00000140009 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92731
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / 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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free:  0.253 (Depositor), 0.251 (DCC) 
  • R-Value Work:  0.232 (Depositor), 0.231 (DCC) 
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
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references, Derived calculations