3HQ5

Progesterone Receptor bound to an Alkylpyrrolidine ligand.

• PDB DOI: https://doi.org/10.2210/pdb3HQ5/pdb

• Classification: hormone binding protein
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-06-05 Released: 2010-03-02 
• Deposition Author(s): Madauss, K.P., Williams, S.P., Washburn, D.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.237 
• R-Value Work: 0.198 
• R-Value Observed: 0.200 

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

• PubMed: 19595590 
• 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.

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Organizational Affiliation: 

Department of Chemistry, Metabolic Pathways Centre for Excellence in Drug Discovery, GlaxoSmithKline Pharmaceuticals, 709 Swedeland Road, King of Prussia, PA 19406, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 60.47 kDa 
• Atom Count: 4,543 
• Modelled Residue Count: 497 
• Deposited Residue Count: 512 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Progesterone receptor	A, B	256	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GKK	G [auth A], I [auth B]	2-chloro-4-{[(3S)-1-methylpyrrolidin-3-yl][2-(trifluoromethyl)benzyl]amino}benzonitrile C20 H19 Cl F3 N3 HMOAZJHSXXENHE-KRWDZBQOSA-N
SO4	C [auth A], D [auth A], E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	H [auth A], J [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
GKK	BindingDB:  3HQ5	IC50: 16 (nM) from 1 assay(s)
		EC50: min: 3, max: 9 (nM) from 2 assay(s)
	Binding MOAD:  3HQ5	IC50: 16 (nM) from 1 assay(s)
	PDBBind:  3HQ5	IC50: 16 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.237 
• R-Value Work: 0.198 
• R-Value Observed: 0.200 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.701	α = 90
b = 64.441	β = 96.51
c = 70.38	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-02 
Deposition Author(s): Madauss, K.P., Williams, S.P., Washburn, D.G.

Revision History  

• Version 1.0: 2010-03-02
  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: 2019-07-24
  Changes: Data collection, Refinement description
• Version 1.4: 2024-02-21
  Changes: Data collection, Database references, Derived calculations