3KBA

Progesterone receptor bound to sulfonamide pyrrolidine partial agonist

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.194 

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

  • 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: 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 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
WOW
Query on WOW
Download SDF File 
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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
WOWEC50: 25 nM (100) BINDINGDB
WOWIC50: 16 nM (100) BINDINGDB
WOWIC50: 16 nM BINDINGMOAD
WOWIC50: 16 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.194 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 57.394α = 90.00
b = 64.349β = 96.53
c = 70.420γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
REFMACrefinement
StructureStudiodata collection
SCALEPACKdata scaling
DENZOdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

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