3G8O

Progesterone Receptor with bound Pyrrolidine 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.204 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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: https://doi.org/10.1016/j.bmcl.2009.06.055
  • Primary Citation of Related Structures:  
    3G8O, 3HQ5

  • 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-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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Progesterone receptor
A, B
263Homo sapiensMutation(s): 0 
Gene Names: NR3C3PGR
UniProt & NIH Common Fund Data Resources
Find proteins for P06401 (Homo sapiens)
Explore P06401 
Go to UniProtKB:  P06401
PHAROS:  P06401
GTEx:  ENSG00000082175 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06401
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
30X
Query on 30X

Download Ideal Coordinates CCD File 
C [auth A],
D [auth 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
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Binding Affinity Annotations 
IDSourceBinding Affinity
30X PDBBind:  3G8O IC50: 125 (nM) from 1 assay(s)
Binding MOAD:  3G8O IC50: 125 (nM) from 1 assay(s)
BindingDB:  3G8O IC50: 125 (nM) from 1 assay(s)
EC50: 1300 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.204 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.67α = 90
b = 64.208β = 96.01
c = 70.5γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-02-16
    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: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description