1YIM

Human estrogen receptor alpha ligand-binding domain in complex with compound 4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.258 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Estrogen receptor ligands. Part 10: Chromanes: old scaffolds for new SERAMs.

Tan, Q.Blizzard, T.A.Morgan, J.D.Birzin, E.T.Chan, W.Yang, Y.T.Pai, L.Y.Hayes, E.C.DaSilva, C.A.Warrier, S.Yudkovitz, J.Wilkinson, H.A.Sharma, N.Fitzgerald, P.M.Li, S.Colwell, L.Fisher, J.E.Adamski, S.Reszka, A.A.Kimmel, D.DiNinno, F.Rohrer, S.P.Freedman, L.P.Schaeffer, J.M.Hammond, M.L.

(2005) Bioorg.Med.Chem.Lett. 15: 1675-1681

  • DOI: 10.1016/j.bmcl.2005.01.046
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The discovery, synthesis, and SAR of chromanes as ER alpha subtype selective ligands are described. X-ray studies revealed that the origin of the ER alpha-selectivity resulted from a C-4 trans methyl substitution to the cis-2,3-diphenyl-chromane plat ...

    The discovery, synthesis, and SAR of chromanes as ER alpha subtype selective ligands are described. X-ray studies revealed that the origin of the ER alpha-selectivity resulted from a C-4 trans methyl substitution to the cis-2,3-diphenyl-chromane platform. Selected compounds from this class demonstrated very potent in vivo antagonism of estradiol in an immature rat uterine weight assay, effectively inhibited ovariectomy-induced bone resorption in a 42 days treatment paradigm, and lowered serum cholesterol levels in ovx'd adult rat models. The best antagonists 8F and 12F also exhibited potent inhibition of MCF-7 cell growth and were shown to be estrogen receptor down-regulators (SERDs).


    Organizational Affiliation

    Department of Medicinal Chemistry, Merck Research Laboratories, PO Box 2000, RY800-B107, Rahway, NJ 07065, USA. qiang_tan@merck.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Estrogen receptor
A
248Homo sapiensMutation(s): 0 
Gene Names: ESR1 (ESR, NR3A1)
Find proteins for P03372 (Homo sapiens)
Go to Gene View: ESR1
Go to UniProtKB:  P03372
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CM4
Query on CM4

Download SDF File 
Download CCD File 
A
(2R,3R,4S)-3-(4-HYDROXYPHENYL)-4-METHYL-2-[4-(2-PYRROLIDIN-1-YLETHOXY)PHENYL]CHROMAN-6-OL
C28 H31 N O4
XPVKGTWRXBSJKO-LHXLBICKSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
CM4IC50: 1.5 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.258 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 58.550α = 90.00
b = 58.550β = 90.00
c = 276.600γ = 120.00
Software Package:
Software NamePurpose
SHELXLrefinement
X-GENdata reduction
X-GENdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-07-26
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description