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


Ligand Structure Quality Assessment 


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
  • Primary Citation of Related Structures:  
    3KBA

  • 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 was intentionally converted to a sulfonamide, carbamate, or amide to address these liabilities ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Progesterone receptorA, B253Homo sapiensMutation(s): 0 
Gene Names: PGRNR3C3
UniProt & NIH Common Fund Data Resources
Find proteins for P06401 (Homo sapiens)
Explore P06401 
Go to UniProtKB:  P06401
PHAROS:  P06401
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
WOW (Subject of Investigation/LOI)
Query on WOW

Download Ideal Coordinates CCD File 
C [auth A], E [auth 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 Ideal Coordinates CCD File 
D [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
WOW Binding MOAD:  3KBA IC50: 16 (nM) from 1 assay(s)
PDBBind:  3KBA IC50: 16 (nM) from 1 assay(s)
BindingDB:  3KBA IC50: 16 (nM) from 1 assay(s)
EC50: 25 (nM) from 1 assay(s)
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



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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