2JJ3

Estrogen receptor beta ligand binding domain in complex with a Benzopyran agonist

• PDB DOI: https://doi.org/10.2210/pdb2JJ3/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-07-03 Released: 2007-08-07 
• Deposition Author(s): 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free: 0.255 
• R-Value Work: 0.235 

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

• PubMed: 17662603 
• DOI: https://doi.org/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. X-ray cocrystal structures with ERalpha and ERbeta are supportive of this approach to improve selectivity in this structural class.

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Organizational Affiliation: 

Discovery Chemistry Research, 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 generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 59.11 kDa 
• Atom Count: 3,630 
• Modelled Residue Count: 451 
• Deposited Residue Count: 514 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ESTROGEN RECEPTOR BETA	A, B	257	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q92731 (Homo sapiens) Explore Q92731  Go to UniProtKB:  Q92731
PHAROS:  Q92731 GTEx:  ENSG00000140009

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JJ3	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

Binding Affinity Annotations
ID	Source	Binding Affinity
JJ3	PDBBind:  2JJ3	Ki: 0.28 (nM) from 1 assay(s)
	BindingDB:  2JJ3	Ki: 0.28 (nM) from 1 assay(s)
	Binding MOAD:  2JJ3	Ki: 0.28 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free: 0.255 
• R-Value Work: 0.235 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.409	α = 90
b = 63.409	β = 90
c = 248.907	γ = 120

Software Package:

Software Name	Purpose
CNX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2007-08-07
  Type: Initial release
  
• Version 1.1: 2011-05-07
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance