4OAR

Progesterone receptor with bound ulipristal acetate and a peptide from the co-repressor SMRT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.211 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Molecular determinants of the recognition of ulipristal acetate by oxo-steroid receptors.

Petit-Topin, I.Fay, M.Resche-Rigon, M.Ulmann, A.Gainer, E.Rafestin-Oblin, M.E.Fagart, J.

(2014) J Steroid Biochem Mol Biol 144PB: 427-435

  • DOI: 10.1016/j.jsbmb.2014.08.008
  • Primary Citation of Related Structures:  
    4OAR

  • PubMed Abstract: 
  • The human progesterone receptor (PR) plays a key role in reproductive function in women. PR antagonists have numerous applications in female health care including regular and emergency contraception, and treatment of hormone-related pathological conditions such as breast cancer, endometriosis, and leiomyoma ...

    The human progesterone receptor (PR) plays a key role in reproductive function in women. PR antagonists have numerous applications in female health care including regular and emergency contraception, and treatment of hormone-related pathological conditions such as breast cancer, endometriosis, and leiomyoma. The main factor limiting their long-term administration is the fact that they cross-bind to other oxo-steroid receptors. Ulipristal acetate (UPA), a highly potent PR antagonist, has recently come onto the market and is much more selective for PR than the other oxo-steroid receptors (androgen, AR, glucocorticoid, GR, and mineralocorticoid, MR receptors) and, remarkably, it displays lower GR-inactivating potency than RU486. We adopted a structural approach to characterizing the binding of UPA to the oxo-steroid receptors at the molecular level. We solved the X-ray crystal structure of the ligand-binding domain (LBD) of the human PR complexed with UPA and a peptide from the transcriptional corepressor SMRT. We used the X-ray crystal structure of the GR in its antagonist conformation to dock UPA within its ligand-binding cavity. Finally, we generated three-dimensional models of the LBD of androgen and mineralocorticoid receptors (AR and MR) in an antagonist conformation and docked UPA within them. Comparing the structures revealed that the network of stabilizing contacts between the UPA C11 aryl group and the LBD is responsible for its high PR antagonist potency. It also showed that it is the inability of UPA to contact Gln642 in GR that explains why it has lower potency in inactivating GR than RU486. Finally, we found that the binding pockets of AR and MR are too small to accommodate UPA, and allowed us to propose that the extremely low sensitivity of MR to UPA is due to inappropriate interactions with the C11 substituent. All these findings open new avenues for designing new PR antagonist compounds displaying greater selectivity.


    Organizational Affiliation

    Inserm U773, Centre de Recherche Biomédicale Bichat-Beaujon CRB3, Paris, France; Université Denis Diderot, Site Bichat, Paris, France; Inserm U693, Le Kremlin - Bicêtre F94276, France; Faculté de Médecine Paris-Sud, Univ Paris-Sud, UMR-S693, Le Kremlin - Bicêtre F94276, France. Electronic address: jerome.fagart@inserm.fr.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Progesterone receptor A258Homo sapiensMutation(s): 0 
Gene Names: NR3C3PGR
Find proteins for P06401 (Homo sapiens)
Explore P06401 
Go to UniProtKB:  P06401
NIH Common Fund Data Resources
PHAROS:  P06401
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Peptide from Nuclear receptor corepressor 2 B17Homo sapiensMutation(s): 0 
Gene Names: NCOR2CTG26
Find proteins for Q9Y618 (Homo sapiens)
Explore Q9Y618 
Go to UniProtKB:  Q9Y618
NIH Common Fund Data Resources
PHAROS:  Q9Y618
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2S0
Query on 2S0

Download Ideal Coordinates CCD File 
A
[(8S,11R,13S,14S,17R)-17-acetyl-11-[4-(dimethylamino)phenyl]-13-methyl-3-oxo-1,2,6,7,8,11,12,14,15,16-decahydrocyclopen ta[a]phenanthren-17-yl] acetate
C30 H37 N O4
OOLLAFOLCSJHRE-ZHAKMVSLSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
2S0IC50:  0.20000000298023224   nM  BindingDB
2S0IC50:  0.03799999877810478   nM  Binding MOAD
2S0EC50:  100   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.211 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.18α = 90
b = 87.18β = 90
c = 90.91γ = 120
Software Package:
Software NamePurpose
MxCuBEdata collection
PHASERphasing
CNSrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-08
    Type: Initial release