3KBA

Progesterone receptor bound to sulfonamide pyrrolidine partial agonist


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Improving the developability profile of pyrrolidine progesterone receptor partial agonists.

Kallander, L.S.Washburn, D.G.Hoang, T.H.Frazee, J.S.Stoy, P.Johnson, L.Lu, Q.Hammond, M.Barton, L.S.Patterson, J.R.Azzarano, L.M.Nagilla, R.Madauss, K.P.Williams, S.P.Stewart, E.L.Duraiswami, C.Grygielko, E.T.Xu, X.Laping, N.J.Bray, J.D.Thompson, S.K.

(2010) Bioorg Med Chem Lett 20: 371-374

  • DOI: 10.1016/j.bmcl.2009.10.092
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The previously reported pyrrolidine class of progesterone receptor partial agonists demonstrated excellent potency but suffered from serious liabilities including hERG blockade and high volume of distribution in the rat. The basic pyrrolidine amine w ...

    The previously reported pyrrolidine class of progesterone receptor partial agonists demonstrated excellent potency but suffered from serious liabilities including hERG blockade and high volume of distribution in the rat. The basic pyrrolidine amine was intentionally converted to a sulfonamide, carbamate, or amide to address these liabilities. The evaluation of the degree of partial agonism for these non-basic pyrrolidine derivatives and demonstration of their efficacy in an in vivo model of endometriosis is disclosed herein.


    Organizational Affiliation

    Department of Chemistry, Metabolic Pathways Centre for Excellence in Drug Discovery, GlaxoSmithKline Pharmaceuticals, 709 Swedeland Road, King of Prussia, PA 19406, USA. lara.s.kallander@gsk.com



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Progesterone receptor
A, B
253Homo 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
WOW
Query on WOW

Download CCD File 
A, B
2-chloro-4-{(2-methylbenzyl)[(3S)-1-(methylsulfonyl)pyrrolidin-3-yl]amino}benzonitrile
C20 H22 Cl N3 O2 S
OTRAFCFYTZJLKH-IBGZPJMESA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
WOWEC50:  25   nM  BindingDB
WOWIC50:  16   nM  Binding MOAD
WOWIC50 :  16   nM  PDBBind
WOWIC50:  16   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.394α = 90
b = 64.349β = 96.53
c = 70.42γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
StructureStudiodata collection

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-12-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description