Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 117.65 kDa 
• Atom Count: 7618 
• Modelled Residue Count: 890 
• Deposited Residue Count: 1016 
• Unique protein chains: 1

1XQC

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

• PDB DOI: 10.2210/pdb1XQC/pdb

• Classification: HORMONE receptor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2004-10-12 Released: 2005-02-01 
• Deposition Author(s): Renaud, J., Bischoff, S.F., Buhl, T., Floersheim, P., Fournier, B., Geiser, M., Halleux, C., Kallen, J., Keller, H.J., Ramage, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.254 
• R-Value Work: 0.211 
• R-Value Observed: 0.213 

Literature

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

• PubMed: 15658851 
• DOI: 10.1021/jm040858p
• Primary Citation of Related Structures:  
  1XQC


• 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.

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Organizational Affiliation: 

Novartis Institute for Biomedical Research, WKL-136.6.81, CH-4002 Basel, Switzerland. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Estrogen receptor	A, B, C, D	254	Homo sapiens	Mutation(s): 3  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
AEJ	E [auth A], F [auth B], G [auth C], H [auth D]	(1S)-1-{4-[(9AR)-OCTAHYDRO-2H-PYRIDO[1,2-A]PYRAZIN-2-YL]PHENYL}-2-PHENYL-1,2,3,4-TETRAHYDROISOQUINOLIN-6-OL C29 H33 N3 O ZGHFWBDHZZKWSI-LITSAYRRSA-N

Binding Affinity Annotations
ID	Source	Binding 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

• Method: X-RAY DIFFRACTION
• 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 = 55.114	α = 90
b = 156.569	β = 90.35
c = 58.962	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-10-12 
• Released Date: 2005-02-01 
Deposition Author(s): Renaud, J., Bischoff, S.F., Buhl, T., Floersheim, P., Fournier, B., Geiser, M., Halleux, C., Kallen, J., Keller, H.J., Ramage, P.

Revision History  

• 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