X-ray structure of ERalpha LBD bound to a tetrahydroisoquinoline SERM ligand at 2.05A resolution

Experimental Data Snapshot

  • Resolution: 2.05 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 

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This is version 1.4 of the entry. See complete history


Selective Estrogen Receptor Modulators with Conformationally Restricted Side Chains. Synthesis and Structure-Activity Relationship of ERalpha-Selective Tetrahydroisoquinoline Ligands

Renaud, J.Bischoff, S.F.Buhl, T.Floersheim, P.Fournier, B.Geiser, M.Halleux, C.Kallen, J.Keller, H.J.Ramage, P.

(2005) J Med Chem 48: 364-379

  • DOI: https://doi.org/10.1021/jm040858p
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    We disclose herein the discovery of estrogen receptor alpha (ERalpha) selective estrogen receptor modulators (SERMs) of the tetrahydroisoquinoline series that incorporate novel conformationally restricted side chains as replacement of the aminoethoxy residue typical of SERMs. Molecular modeling studies used in conjunction with the X-ray crystal structure of the ERalpha ligand binding domain (LBD) with raloxifene (7) suggested a diazadecaline moiety as a viable mimic of the SERM side chain. On the basis of this knowledge, the piperidinylethoxy moiety of our lead compound 60 was replaced by a diazadecaline subunit, providing the novel tetrahydroisoquinoline 29. In addition to exhibiting a binding affinity to ERalpha and antagonistic properties in the estrogen response element and MCF-7 assays similar to those of the parent compound 60, ligand 29 showed a reduced agonist behavior in the MCF-7 assay in the absence of 17beta-estradiol. These data point toward the fact that 29 may have a potential for breast cancer prevention/treatment in vivo, a feature which is particularly attractive in the quest for safe alternatives to hormone replacement therapy. In a pharmacokinetic experiment carried out in rats, 29 displayed an interesting profile, with a bioavailability of 49%. We also disclose the X-ray crystal structure of 29 in complex with ERalpha-LBD, which reveals the preferred configurations of 29 at the two chiral centers and the details of its interactions with the receptor. Finally, our structure-activity relationship studies show that other analogues bearing constrained side chains retain potency and antagonist activity and that a 3-OH substituted phenyl D-ring increases the selectivity of a set of piperazinyl-containing ligands in favor of ERalpha over ERbeta.

  • Organizational Affiliation

    Novartis Institute for Biomedical Research, WKL-136.6.81, CH-4002 Basel, Switzerland. johanne.renaud@pharma.novartis.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Estrogen receptor
A, B, C, D
254Homo sapiensMutation(s): 3 
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
Binding Affinity Annotations 
IDSourceBinding Affinity
AEJ PDBBind:  1XQC IC50: 63 (nM) from 1 assay(s)
BindingDB:  1XQC IC50: 63 (nM) from 1 assay(s)
EC50: 23.2 (nM) from 1 assay(s)
Binding MOAD:  1XQC IC50: 63 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.05 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.114α = 90
b = 156.569β = 90.35
c = 58.962γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-02-01
    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: 2021-11-10
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-10-25
    Changes: Data collection, Refinement description