1XP9

HUMAN ESTROGEN RECEPTOR ALPHA LIGAND-BINDING DOMAIN IN COMPLEX WITH COMPOUND 18


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.299 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Estrogen receptor ligands. Part 9: Dihydrobenzoxathiin SERAMs with alkyl substituted pyrrolidine side chains and linkers.

Blizzard, T.A.Dininno, F.Morgan, J.D.Chen, H.Y.Wu, J.Y.Kim, S.Chan, W.Birzin, E.T.Yang, Y.T.Pai, L.Y.Fitzgerald, P.M.Sharma, N.Li, Y.Zhang, Z.Hayes, E.C.Dasilva, C.A.Tang, W.Rohrer, S.P.Schaeffer, J.M.Hammond, M.L.

(2005) Bioorg Med Chem Lett 15: 107-113

  • DOI: https://doi.org/10.1016/j.bmcl.2004.10.036
  • Primary Citation of Related Structures:  
    1XP1, 1XP6, 1XP9, 1XPC

  • PubMed Abstract: 

    A series of dihydrobenzoxathiin SERAMs with alkylated pyrrolidine side chains or alkylated linkers was prepared. Minor modifications in the side chain or linker resulted in significant effects on biological activity, especially in uterine tissue.


  • Organizational Affiliation

    Merck Research Laboratories, RY800-B116, PO Box 2000, Rahway, NJ 07065, USA. tim_blizzard@merck.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Estrogen receptor248Homo sapiensMutation(s): 0 
Gene Names: ESR1NR3A1ESR
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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AIJ
Query on AIJ

Download Ideal Coordinates CCD File 
B [auth A](2S,3R)-3-(4-HYDROXYPHENYL)-2-(4-{[(2S)-2-PYRROLIDIN-1-YLPROPYL]OXY}PHENYL)-2,3-DIHYDRO-1,4-BENZOXATHIIN-6-OL
C27 H29 N O4 S
UZOOIPXOYYJULJ-RHLLTPQKSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
AIJ Binding MOAD:  1XP9 IC50: 1.3 (nM) from 1 assay(s)
PDBBind:  1XP9 IC50: 1.3 (nM) from 1 assay(s)
BindingDB:  1XP9 IC50: 1.3 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.299 
  • R-Value Observed: 0.187 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.64α = 90
b = 58.64β = 90
c = 275.77γ = 120
Software Package:
Software NamePurpose
X-GENdata scaling
X-GENdata reduction
SHELXLrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-12-07
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2024-02-14
    Changes: Data collection, Database references, Derived calculations