1U9E

CRYSTAL STRUCTURE OF ESTROGEN RECEPTOR BETA COMPLEXED WITH WAY-397

• PDB DOI: https://doi.org/10.2210/pdb1U9E/pdb

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


• Deposited: 2004-08-09 Released: 2005-03-01 
• Deposition Author(s): Manas, E.S., Unwalla, R.J., Xu, Z.B., Malamas, M.S., Miller, C.P., Harris, H.A., Hsiao, C., Akopian, T., Hum, W.T., Malakian, K., Wolfrom, S., Bapat, A., Bhat, R.A., Stahl, M.L., Somers, W.S., Alvarez, J.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.279 
• R-Value Work: 0.231 
• R-Value Observed: 0.234 

Starting Model: experimental

Literature

Structure-Based Design Of Estrogen Receptor-beta Selective Ligands

Manas, E.S., Unwalla, R.J., Xu, Z.B., Malamas, M.S., Miller, C.P., Harris, H.A., Hsiao, C., Akopian, T., Hum, W.T., Malakian, K., Wolfrom, S., Bapat, A., Bhat, R.A., Stahl, M.L., Somers, W.S., Alvarez, J.C.

(2004) J Am Chem Soc 126: 15106-15119

• PubMed: 15548008 
• DOI: https://doi.org/10.1021/ja047633o
• Primary Citation of Related Structures:  
  1U9E, 1X76, 1X78, 1X7B, 1X7E


• PubMed Abstract: 
  

  We present the structure-based optimization of a series of estrogen receptor-beta (ERbeta) selective ligands. X-ray cocrystal structures of these ligands complexed to both ERalpha and ERbeta are described. We also discuss how molecular modeling was used to take advantage of subtle differences between the two binding cavities in order to optimize selectivity for ERbeta over ERalpha. Quantum chemical calculations are utilized to gain insight into the mechanism of selectivity enhancement. Despite only two relatively conservative residue substitutions in the ligand binding pocket, the most selective compounds have greater than 100-fold selectivity for ERbeta relative to ERalpha when measured using a competitive radioligand binding assay.

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Organizational Affiliation: 

Department of Chemical and Screening Sciences, Wyeth Research, 500 Arcola Road, Collegeville, Pennsylvania 19426, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 57.02 kDa 
• Atom Count: 3,848 
• Modelled Residue Count: 469 
• Deposited Residue Count: 500 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Estrogen receptor beta	A, B	241	Homo sapiens	Mutation(s): 0  Gene Names: ESR2, NR3A2, ESTRB
UniProt & NIH Common Fund Data Resources
Find proteins for Q92731 (Homo sapiens) Explore Q92731  Go to UniProtKB:  Q92731
PHAROS:  Q92731 GTEx:  ENSG00000140009

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
STEROID RECEPTOR COACTIVATOR-1	C, D	9	N/A	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
397	E [auth A], F [auth B]	2-(4-HYDROXY-PHENYL)BENZOFURAN-5-OL C14 H10 O3 SNNNDCMXZYWCCI-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
397	BindingDB:  1U9E	IC50: 6 (nM) from 1 assay(s)
		EC50: 5.7 (nM) from 1 assay(s)
	PDBBind:  1U9E	IC50: 5.7 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.279 
• R-Value Work: 0.231 
• R-Value Observed: 0.234 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.113	α = 90
b = 87.935	β = 90
c = 99.524	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-03-01 
Deposition Author(s): Manas, E.S., Unwalla, R.J., Xu, Z.B., Malamas, M.S., Miller, C.P., Harris, H.A., Hsiao, C., Akopian, T., Hum, W.T., Malakian, K., Wolfrom, S., Bapat, A., Bhat, R.A., Stahl, M.L., Somers, W.S., Alvarez, J.C.

Revision History  

• Version 1.0: 2005-03-01
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-04-03
  Changes: Refinement description