Human estrogen receptor alpha ligand-binding domain in complex with compound 1D

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.323 
  • R-Value Observed: 0.215 

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This is version 1.2 of the entry. See complete history


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

  • 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.

  • Organizational Affiliation

    Department of Medicinal Chemistry, Merck Research Laboratories, PO Box 2000, 800B-109 Rahway, NJ 07065, USA. kevin_dykstra@merck.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Estrogen receptor
A, B
254Homo sapiensMutation(s): 0 
Gene Names: ESR1ESRNR3A1
UniProt & NIH Common Fund Data Resources
Find proteins for P03372 (Homo sapiens)
Explore P03372 
Go to UniProtKB:  P03372
PHAROS:  P03372
GTEx:  ENSG00000091831 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03372
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on IOK

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C26 H26 N2 O2
Binding Affinity Annotations 
IDSourceBinding Affinity
IOK Binding MOAD:  2IOK IC50: 1 (nM) from 1 assay(s)
BindingDB:  2IOK IC50: 1 (nM) from 1 assay(s)
PDBBind:  2IOK IC50: 1 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.323 
  • R-Value Observed: 0.215 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.86α = 90
b = 99.86β = 90
c = 54.9γ = 90
Software Package:
Software NamePurpose

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-10-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description