2GIU

Human estrogen receptor beta ligand-binding domain in complex with compound 45

• PDB DOI: https://doi.org/10.2210/pdb2GIU/pdb

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


• Deposited: 2006-03-29 Released: 2006-10-10 
• Deposition Author(s): Fitzgerald, P.M.D., Sharma, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.323 
• R-Value Work: 0.227 
• R-Value Observed: 0.227 

Starting Model: experimental

Literature

The discovery of tetrahydrofluorenones as a new class of estrogen receptor beta-subtype selective ligands.

Wilkening, R.R., Ratcliffe, R.W., Tynebor, E.C., Wildonger, K.J., Fried, A.K., Hammond, M.L., Mosley, R.T., Fitzgerald, P.M.D., Sharma, N., McKeever, B.M., Nilsson, S., Carlquist, M., Thorsell, A., Locco, L., Katz, R., Frisch, K., Birzin, E.T., Wilkinson, H.A., Mitra, S., Cai, S., Hayes, E.C., Schaeffer, J.M., Rohrer, S.P.

(2006) Bioorg Med Chem Lett 16: 3489-3494

• PubMed: 16632357 
• DOI: https://doi.org/10.1016/j.bmcl.2006.03.098
• Primary Citation of Related Structures:  
  2GIU


• PubMed Abstract: 
  

  Synthesis and derivatization of a series of substituted tetrahydrofluorenone analogs giving potent, ERbeta subtype selective ligands are described. Several analogs possessing ERbeta binding affinities comparable to 17beta-estradiol but with greater than 75-fold selectivity over ERalpha are reported.

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Organizational Affiliation: 

Department of Medicinal Chemistry, Merck Research Laboratories, PO Box 2000, Rahway, NJ 07065, 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: 27.56 kDa 
• Atom Count: 1,840 
• Modelled Residue Count: 225 
• Deposited Residue Count: 241 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Estrogen receptor beta	A	241	Homo sapiens	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FBR	B [auth A]	(9aS)-4-bromo-9a-butyl-7-hydroxy-1,2,9,9a-tetrahydro-3H-fluoren-3-one C17 H19 Br O2 FTEBGBCQCYMDPH-KRWDZBQOSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
FBR	PDBBind:  2GIU	IC50: 1.5 (nM) from 1 assay(s)
	BindingDB:  2GIU	IC50: min: 1.5, max: 1.8 (nM) from 2 assay(s)
		EC50: 4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.323 
• R-Value Work: 0.227 
• R-Value Observed: 0.227 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.53	α = 90
b = 64.53	β = 90
c = 251.16	γ = 120

Software Package:

Software Name	Purpose
X-GEN	data scaling
X-GEN	data reduction
SHELXL	refinement
MAR345	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-10-10 
Deposition Author(s): Fitzgerald, P.M.D., Sharma, N.

Revision History  

• Version 1.0: 2006-10-10
  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: 2024-02-14
  Changes: Data collection, Database references, Derived calculations
• Version 1.5: 2024-04-03
  Changes: Refinement description