3HQ5

Progesterone Receptor bound to an Alkylpyrrolidine ligand.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.3 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
  • Structures With Same Primary Citation

  • 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
256Homo sapiensMutation(s): 0 
Gene Names: PGRNR3C3
Find proteins for P06401 (Homo sapiens)
Go to UniProtKB:  P06401
NIH Common Fund Data Resources
PHAROS  P06401
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GKK
Query on GKK

Download CCD File 
A, B
2-chloro-4-{[(3S)-1-methylpyrrolidin-3-yl][2-(trifluoromethyl)benzyl]amino}benzonitrile
C20 H19 Cl F3 N3
HMOAZJHSXXENHE-KRWDZBQOSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A, B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GKKIC50 :  16   nM  PDBBind
GKKEC50:  9   nM  BindingDB
GKKIC50:  16   nM  Binding MOAD
GKKEC50:  3   nM  BindingDB
GKKIC50:  16   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.701α = 90
b = 64.441β = 96.51
c = 70.38γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
DENZOdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-03-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2019-07-24
    Changes: Data collection, Refinement description