3KBA

Progesterone receptor bound to sulfonamide pyrrolidine partial agonist

• PDB DOI: https://doi.org/10.2210/pdb3KBA/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-10-20 Released: 2009-12-08 
• Deposition Author(s): Kallander, L.S., Washburn, D.G., Williams, S.P., Madauss, K.P.

---

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 

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

• PubMed: 19926282 
• DOI: https://doi.org/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 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. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 59.41 kDa 
• Atom Count: 4,514 
• Modelled Residue Count: 494 
• Deposited Residue Count: 506 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Progesterone receptor	A, B	253	Homo sapiens	Mutation(s): 0  Gene Names: PGR, NR3C3
UniProt & NIH Common Fund Data Resources
Find proteins for P06401 (Homo sapiens) Explore P06401  Go to UniProtKB:  P06401
PHAROS:  P06401 GTEx:  ENSG00000082175

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
WOW	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
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
WOW	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 = 57.394	α = 90
b = 64.349	β = 96.53
c = 70.42	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
StructureStudio	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-12-08 
Deposition Author(s): Kallander, L.S., Washburn, D.G., Williams, S.P., Madauss, K.P.

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
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references, Derived calculations