1NDE

Estrogen Receptor beta with Selective Triazine Modulator

• PDB DOI:  https://doi.org/10.2210/pdb1NDE/pdb

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


• Deposited: 2002-12-09 Released: 2002-12-18 
• Deposition Author(s): Henke, B.R., Consler, T.G., Go, N., Hale, R.L., Hohman, D.R., Jones, S.A., Lu, A.T., Moore, L.B., Moore, J.T., Orband-Miller, L.A., Robinett, R.G., Shearin, J., Spearing, P.K., Stewart, E.L., Turnbull, P.S., Weaver, S.L., Williams, S.P., Wisely, G.B., Lambert, M.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.273 
• R-Value Work: 0.240 
• R-Value Observed: 0.240 

Literature

A New Series of Estrogen Receptor Modulators That Display Selectivity for Estrogen Receptor beta

Henke, B.R., Consler, T.G., Go, N., Hale, R.L., Hohman, D.R., Jones, S.A., Lu, A.T., Moore, L.B., Moore, J.T., Orband-Miller, L.A., Robinett, R.G., Shearin, J., Spearing, P.K., Stewart, E.L., Turnbull, P.S., Weaver, S.L., Williams, S.P., Wisely, G.B., Lambert, M.H.

(2002) J Med Chem 45: 5492-5505

• PubMed: 12459017 
• DOI: https://doi.org/10.1021/jm020291h
• Primary Citation of Related Structures:  
  1NDE


• PubMed Abstract: 
  

A series of 1,3,5-triazine-based estrogen receptor (ER) modulators that are modestly selective for the ERbeta subtype are reported. Compound 1, which displayed modest potency and selectivity for ERbeta vs ERalpha, was identified via high-throughput screening utilizing an ERbeta SPA-based binding assay. Subsequent analogue preparation resulted in the identification of compounds such as 21 and 43 that display 25- to 30-fold selectivity for ERbeta with potencies in the 10-30 nM range. These compounds profile as full antagonists at ERbeta and weak partial agonists at ERalpha in a cell-based reporter gene assay. In addition, the X-ray crystal structure of compound 15 complexed with the ligand binding domain of ERbeta has been solved and was utilized in the design of more conformationally restrained analogues such as 31 in an attempt to increase selectivity for the ERbeta subtype.

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Organizational Affiliation: 

GlaxoSmithKline Research and Development, Research Triangle Park, North Carolina 27709, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA,PQS (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 29.6 kDa 
• Atom Count: 1,864 
• Modelled Residue Count: 231 
• Deposited Residue Count: 255 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Estrogen receptor beta	A	255	Homo sapiens	Mutation(s): 0  Gene Names: ESTRB, ESR2, 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
MON	B [auth A]	4-(2-{[4-{[3-(4-CHLOROPHENYL)PROPYL]SULFANYL}-6-(1-PIPERAZINYL)-1,3,5-TRIAZIN-2-YL]AMINO}ETHYL)PHENOL C24 H29 Cl N6 O S AIBKIFHSQQYXLG-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
MON	BindingDB:  1NDE	Ki: 15 (nM) from 1 assay(s)
		IC50: 6 (nM) from 1 assay(s)
	PDBBind:  1NDE	Ki: 15 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.273 
• R-Value Work: 0.240 
• R-Value Observed: 0.240 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.558	α = 90
b = 65.558	β = 90
c = 239.3	γ = 120

Software Package:

Software Name	Purpose
MAR345	data collection
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-12-18 
Deposition Author(s): Henke, B.R., Consler, T.G., Go, N., Hale, R.L., Hohman, D.R., Jones, S.A., Lu, A.T., Moore, L.B., Moore, J.T., Orband-Miller, L.A., Robinett, R.G., Shearin, J., Spearing, P.K., Stewart, E.L., Turnbull, P.S., Weaver, S.L., Williams, S.P., Wisely, G.B., Lambert, M.H.

Revision History  

• Version 1.0: 2002-12-18
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2023-08-16
  Changes: Data collection, Database references, Derived calculations, Refinement description