2POG

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

• PDB DOI: https://doi.org/10.2210/pdb2POG/pdb

• Classification: LIPID BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-04-26 Released: 2007-09-11 
• Deposition Author(s): Richardson, T.I., Norman, B.H., Lugar, C.W., Jones, S.A., Wang, Y., Durbin, J.D., Krishnan, V., Dodge, J.A.

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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 

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

• PubMed: 17485205 
• 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.

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Organizational Affiliation: 

Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN 46285, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 57.16 kDa 
• Atom Count: 3,705 
• Modelled Residue Count: 444 
• Deposited Residue Count: 496 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Estrogen receptor	A, B	248	Homo sapiens	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
WST	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
ID	Source	Binding 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 = 60.584	α = 90
b = 99.81	β = 90
c = 173.098	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CNX	phasing
CNX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-09-11 
Deposition Author(s): Richardson, T.I., Norman, B.H., Lugar, C.W., Jones, S.A., Wang, Y., Durbin, J.D., Krishnan, V., Dodge, J.A.

Revision History  

• 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