2QTU

Estrogen receptor beta ligand-binding domain complexed to a benzopyran ligand

• PDB DOI: https://doi.org/10.2210/pdb2QTU/pdb

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


• Deposited: 2007-08-02 Released: 2007-10-30 
• Deposition Author(s): Richardson, T.I., Dodge, J.A., Wang, Y., Durbin, J.D., Krishnan, V., Norman, B.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.53 Å
• R-Value Free: 0.279 
• R-Value Work: 0.264 

Literature

Benzopyrans as selective estrogen receptor beta agonists (SERBAs). Part 5: Combined A- and C-ring structure-activity relationship studies.

Richardson, T.I., Dodge, J.A., Wang, Y., Durbin, J.D., Krishnan, V., Norman, B.H.

(2007) Bioorg Med Chem Lett 17: 5563-5566

• PubMed: 17804226 
• DOI: https://doi.org/10.1016/j.bmcl.2007.08.009
• Primary Citation of Related Structures:  
  2QTU


• 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 synthesis of a late stage intermediate that allowed us to combine A-ring and C-ring modifications and carry out simultaneous SAR studies at both positions. Modification of both positions proved additive, maintaining affinity and improving ERbeta selectivity up to 83-fold. An X-ray cocrystal structure confirms the previously observed binding mode in ERbeta.

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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 and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 59.18 kDa 
• Atom Count: 3,514 
• Modelled Residue Count: 441 
• 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  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 GTEx:  ENSG00000140009

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3AS	C [auth A], D [auth B]	(3aS,4R,9bR)-2,2-difluoro-4-(4-hydroxyphenyl)-6-(methoxymethyl)-1,2,3,3a,4,9b-hexahydrocyclopenta[c]chromen-8-ol C20 H20 F2 O4 GPFRMIHXGMVMGF-BZSNNMDCSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
3AS	PDBBind:  2QTU	Ki: 0.53 (nM) from 1 assay(s)
	BindingDB:  2QTU	Ki: 0.53 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.53 Å
• R-Value Free: 0.279 
• R-Value Work: 0.264 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.798	α = 90
b = 63.798	β = 90
c = 249.616	γ = 120

Software Package:

Software Name	Purpose
CNX	refinement
MAR345dtb	data collection
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-10-30 
Deposition Author(s): Richardson, T.I., Dodge, J.A., Wang, Y., Durbin, J.D., Krishnan, V., Norman, B.H.

Revision History  

• Version 1.0: 2007-10-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations