1UOM

The Structure of Estrogen Receptor in Complex with a Selective and Potent Tetrahydroisochiolin Ligand.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 
    0.287 (Depositor), 0.280 (DCC) 
  • R-Value Work: 
    0.235 (Depositor), 0.230 (DCC) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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This is version 1.3 of the entry. See complete history


Literature

Estrogen Receptor Modulators: Identification and Structure-Activity Relationships of Potent Eralpha-Selective Tetrahydroisoquinoline Ligands

Renaud, J.Bischoff, S.F.Buhl, T.Floersheim, P.Fournier, B.Halleux, C.Kallen, J.Keller, H.Schlaeppi, J.-M.Stark, W.

(2003) J Med Chem 46: 2945

  • DOI: https://doi.org/10.1021/jm030086h
  • Primary Citation of Related Structures:  
    1UOM

  • PubMed Abstract: 

    As part of a program aimed at the development of selective estrogen receptor modulators (SERMs), tetrahydroisoquinoline derivative 27 was discovered by high throughput screening. Successive replacements of the p-F substituent of 27 by an aminoethoxy side chain and of the 1-H of the tetrahydroisoquinoline core by a 1-Me group provided analogues 19 and 20. These compounds showed potencies in a cell-based reporter gene assay (ERE assay) varying between 0.6 and 20 nM and displayed antagonist behaviors in the MCF-7 human breast adenocarcinoma cell line with IC(50)s in the range of 2-36 nM. The effect of N-phenyl substituents on the activity and pharmacokinetic properties of tetrahydroisoquinoline analogues was explored. As a result of this investigation, two potent derivatives bearing a p-F N-aryl group, 19c and 20c, were discovered as candidates suitable for further profiling. To gain insight into the ligand-receptor interaction, the X-ray crystallographic structure of the 1-H tetrahydroisoquinoline derivative (R)-18a in complex with ERalpha-ligand binding domain (LBD)(301)(-)(553)/C-->S triple mutant was solved to 2.28 A. An overlay of this X-ray crystal structure with that reported for the complex of ERalpha-LBD(301)(-)(553)/carboxymethylated C and raloxifene (5) shows that both compounds bind to the same cleft of the receptor and display comparable binding modes, with differences being observed in the conformation of their "D-ring" phenyl groups.


  • Organizational Affiliation

    Novartis Pharma Research, WKL-136.3.25, CH-4002 Basel, Switzerland. johanne.renaud@pharma.novartis.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ESTROGEN RECEPTOR254Homo 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
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PTI
Query on PTI

Download Ideal Coordinates CCD File 
B [auth A]2-PHENYL-1-[4-(2-PIPERIDIN-1-YL-ETHOXY)-PHENYL]-1,2,3,4-TETRAHYDRO-ISOQUINOLIN-6-OL
C28 H32 N2 O2
FMWVCTJKLAVRPB-MUUNZHRXSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
PTI BindingDB:  1UOM IC50: min: 16.48, max: 19.01 (nM) from 3 assay(s)
EC50: 16.5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free:  0.287 (Depositor), 0.280 (DCC) 
  • R-Value Work:  0.235 (Depositor), 0.230 (DCC) 
Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.2α = 90
b = 58.2β = 90
c = 274.6γ = 120
Software Package:
Software NamePurpose
CNXrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted PTIClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-07-03
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Other, Refinement description