3G8O

Progesterone Receptor with bound Pyrrolidine 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Rational design of orally-active, pyrrolidine-based progesterone receptor partial agonists.

Thompson, S.K.Washburn, D.G.Frazee, J.S.Madauss, K.P.Hoang, T.H.Lapinski, L.Grygielko, E.T.Glace, L.E.Trizna, W.Williams, S.P.Duraiswami, C.Bray, J.D.Laping, N.J.

(2009) Bioorg.Med.Chem.Lett. 19: 4777-4780

  • DOI: 10.1016/j.bmcl.2009.06.055
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Using the X-ray crystal structure of an amide-based progesterone receptor (PR) partial agonist bound to the PR ligand binding domain, a novel PR partial agonist class containing a pyrrolidine ring was designed. Members of this class of N-alkylpyrroli ...

    Using the X-ray crystal structure of an amide-based progesterone receptor (PR) partial agonist bound to the PR ligand binding domain, a novel PR partial agonist class containing a pyrrolidine ring was designed. Members of this class of N-alkylpyrrolidines demonstrate potent and highly selective partial agonism of the progesterone receptor, and one of these analogs was shown to be efficacious upon oral dosing in the OVX rat model of estrogen opposition.


    Organizational Affiliation

    Department of Chemistry, Metabolic Pathways Centre for Excellence in Drug Discovery, GlaxoSmithKline Pharmaceuticals, 709 Swedeland Road, King of Prussia, PA 19406, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Progesterone receptor
A, B
263Homo sapiensMutation(s): 0 
Gene Names: PGR (NR3C3)
Find proteins for P06401 (Homo sapiens)
Go to Gene View: PGR
Go to UniProtKB:  P06401
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
30X
Query on 30X

Download SDF File 
Download CCD File 
A, B
N~2~-[4-cyano-3-(trifluoromethyl)phenyl]-N,N-dimethyl-N~2~-(2,2,2-trifluoroethyl)-L-alaninamide
C15 H15 F6 N3 O
BEFAEFLFXOZVJY-VIFPVBQESA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
30XEC50: 1300 nM (100) BINDINGDB
30XIC50: 125 nM (100) BINDINGDB
30XIC50: 125 nM BINDINGMOAD
30XIC50: 125 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.204 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 57.670α = 90.00
b = 64.208β = 96.01
c = 70.500γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
DENZOdata reduction
CNSrefinement
ADSCdata collection
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
AMoREphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-02-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description