2IOG

Human estrogen receptor alpha ligand-binding domain in complex with compound 11F

• PDB DOI: https://doi.org/10.2210/pdb2IOG/pdb

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


• Deposited: 2006-10-10 Released: 2007-10-09 
• Deposition Author(s): Fitzgerald, P.M.D., Sharma, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.328 
• R-Value Observed: 0.212 

Literature

Estrogen receptor ligands. Part 16: 2-Aryl indoles as highly subtype selective ligands for ERalpha

Dykstra, K.D., Guo, L., Birzin, E.T., Chan, W., Yang, Y.T., Hayes, E.C., DaSilva, C.A., Pai, L.-Y., Mosley, R.T., Kraker, B., Fitzgerald, P.M.D., DiNinno, F., Rohrer, S.P., Schaeffer, J.M., Hammond, M.L.

(2007) Bioorg Med Chem Lett 17: 2322-2328

• PubMed: 17289385 
• DOI: https://doi.org/10.1016/j.bmcl.2007.01.054
• Primary Citation of Related Structures:  
  2IOG, 2IOK


• PubMed Abstract: 
  

  A novel class of indole ligands for estrogen receptor alpha have been discovered which exhibit potent affinity and high selectivity. Substitution of the bazedoxifene skeleton to the linker present in the HTS lead 1a provided 22b which was found to be 130-fold alpha-selective and acted as an antagonist of estradiol activity in uterine tissue and MCF-7 cancer cells.

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Organizational Affiliation: 

Department of Medicinal Chemistry, Merck Research Laboratories, PO Box 2000, 800B-109 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 and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 28.66 kDa 
• Atom Count: 2,161 
• Modelled Residue Count: 243 
• Deposited Residue Count: 246 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Estrogen receptor	A	246	Homo sapiens	Mutation(s): 0  Gene Names: ESR1, ESR, NR3A1
UniProt & NIH Common Fund Data Resources
Find proteins for P03372 (Homo sapiens) Explore P03372  Go to UniProtKB:  P03372
PHAROS:  P03372 GTEx:  ENSG00000091831

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IOG	B [auth A]	N-[(1R)-3-(4-HYDROXYPHENYL)-1-METHYLPROPYL]-2-[2-PHENYL-6-(2-PIPERIDIN-1-YLETHOXY)-1H-INDOL-3-YL]ACETAMIDE C33 H39 N3 O3 FACGWONUFWMXPN-XMMPIXPASA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
IOG	PDBBind:  2IOG	IC50: 8 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.328 
• R-Value Observed: 0.212 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.22	α = 90
b = 58.22	β = 90
c = 276.66	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-10-09 
Deposition Author(s): Fitzgerald, P.M.D., Sharma, N.

Revision History  

• Version 1.0: 2007-10-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-07-07
  Changes: Derived calculations, Refinement description
• Version 1.3: 2021-07-28
  Changes: Refinement description
• Version 1.4: 2024-02-21
  Changes: Data collection, Database references