2I0G

Benzopyrans are Selective Estrogen Receptor beta Agonists (SERBAs) with Novel Activity in Models of Benign Prostatic Hyperplasia

• PDB DOI:  https://doi.org/10.2210/pdb2I0G/pdb

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


• Deposited: 2006-08-10 Released: 2006-10-24 
• Deposition Author(s): Wang, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.271 
• R-Value Work: 0.233 
• R-Value Observed: 0.235 

Literature

Benzopyrans are selective estrogen receptor Beta agonists with novel activity in models of benign prostatic hyperplasia.

Norman, B.H., Dodge, J.A., Richardson, T.I., Borromeo, P.S., Lugar, C.W., Jones, S.A., Chen, K., Wang, Y., Durst, G.L., Barr, R.J., Montrose-Rafizadeh, C., Osborne, H.E., Amos, R.M., Guo, S., Boodhoo, A., Krishnan, V.

(2006) J Med Chem 49: 6155-6157

• PubMed: 17034120 
• DOI: https://doi.org/10.1021/jm060491j
• Primary Citation of Related Structures:  
  2I0G, 2I0J


• PubMed Abstract: 
  

Benzopyran selective estrogen receptor beta agonist-1 (SERBA-1) shows potent, selective binding and agonist function in estrogen receptor beta (ERbeta) in vitro assays. X-ray crystal structures of SERBA-1 in ERalpha and beta help explain observed beta-selectivity of this ligand. SERBA-1 in vivo demonstrates involution of the ventral prostate in CD-1 mice (ERbeta effect), while having no effect on gonadal hormone levels (ERalpha effect) at 10x the efficacious dose, consistent with in vitro properties of this molecule.

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Organizational Affiliation: 

Discovery Chemistry Research, Bone and Inflammation Research, Lead Optimization Biology, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, USA. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 59.02 kDa 
• Atom Count: 3,532 
• Modelled Residue Count: 443 
• 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
I0G	C [auth A], D [auth B]	(3AS,4R,9BR)-4-(4-HYDROXYPHENYL)-1,2,3,3A,4,9B-HEXAHYDROCYCLOPENTA[C]CHROMEN-8-OL C18 H18 O3 XIESSJVMWNJCGZ-VKJFTORMSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
I0G	BindingDB:  2I0G	Ki: min: 0.17, max: 0.47 (nM) from 3 assay(s)
		EC50: 0.66 (nM) from 1 assay(s)
	Binding MOAD:  2I0G	Ki: 0.19 (nM) from 1 assay(s)
	PDBBind:  2I0G	Ki: 0.19 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.271 
• R-Value Work: 0.233 
• R-Value Observed: 0.235 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.196	α = 90
b = 63.196	β = 90
c = 249.255	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
AMoRE	phasing
CNX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-10-24 
Deposition Author(s): Wang, Y.

Revision History  

• Version 1.0: 2006-10-24
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description