2W8Y

RU486 bound to the progesterone receptor in a destabilized agonistic conformation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The X-Ray Structure of Ru486 Bound to the Progesterone Receptor in a Destabilized Agonistic Conformation.

Raaijmakers, H.C.A.Versteegh, J.Uitdehaag, J.C.M.

(2009) J Biol Chem 284: 19572

  • DOI: 10.1074/jbc.M109.007872
  • Primary Citation of Related Structures:  
    2W8Y

  • PubMed Abstract: 
  • Here we describe the 1.95 A structure of the clinically used antiprogestin RU486 (mifepristone) in complex with the progesterone receptor (PR). The structure was obtained by taking a crystal of the PR ligand binding domain containing the agonist norethindrone and soaking it in a solution containing the antagonist RU486 for extended times ...

    Here we describe the 1.95 A structure of the clinically used antiprogestin RU486 (mifepristone) in complex with the progesterone receptor (PR). The structure was obtained by taking a crystal of the PR ligand binding domain containing the agonist norethindrone and soaking it in a solution containing the antagonist RU486 for extended times. Clear ligand exchange could be observed in one copy of the PR ligand binding domain dimer in the crystal. RU486 binds while PR is in an agonistic conformation without displacing helix 12. Although this is probably because of the constraints of the crystal lattice, it demonstrates that helix 12 displacement is not a prerequisite for RU486 binding. Interestingly, B-factor analysis clearly shows that helix 12 becomes more flexible after RU486 binding, suggesting that RU486, being a model antagonist, does not induce one fixed conformation of helix 12 but changes its positional equilibrium. This conclusion is confirmed by comparing the structures of RU486 bound to PR and RU486 bound to the glucocorticoid receptor.


    Organizational Affiliation

    Departments of Molecular Design and Informatics, Molecular Pharmacology and DMPK, Schering-Plough Research Institute, P. O. Box 20, 5340 BH Oss, The Netherlands.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROGESTERONE RECEPTORA, B260Homo sapiensMutation(s): 0 
Gene Names: PGRNR3C3
Find proteins for P06401 (Homo sapiens)
Explore P06401 
Go to UniProtKB:  P06401
NIH Common Fund Data Resources
PHAROS:  P06401
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
486
Query on 486

Download Ideal Coordinates CCD File 
C [auth A]11-(4-DIMETHYLAMINO-PHENYL)-17-HYDROXY-13-METHYL-17-PROP-1-YNYL-1,2,6,7,8,11,12,13,14,15,16,17-DODEC AHYDRO-CYCLOPENTA[A]PHENANTHREN-3-ONE
C29 H35 N O2
VKHAHZOOUSRJNA-GCNJZUOMSA-N
 Ligand Interaction
NDR
Query on NDR

Download Ideal Coordinates CCD File 
E [auth B](14beta,17alpha)-17-ethynyl-17-hydroxyestr-4-en-3-one
C20 H26 O2
VIKNJXKGJWUCNN-XGXHKTLJSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
F [auth B]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
486IC50:  0.03999999910593033   nM  BindingDB
486Ki:  0.25   nM  BindingDB
486IC50:  3   nM  BindingDB
486Ki:  0.5799999833106995   nM  BindingDB
NDRIC50:  3.200000047683716   nM  BindingDB
486IC50:  1.399999976158142   nM  BindingDB
486Ki:  1.100000023841858   nM  BindingDB
486IC50:  0.18000000715255737   nM  BindingDB
486IC50:  0.05000000074505806   nM  BindingDB
486Ki:  0.6399999856948853   nM  BindingDB
486IC50:  5.199999809265137   nM  BindingDB
486IC50:  0.019999999552965164   nM  BindingDB
NDREC50:  2.200000047683716   nM  BindingDB
486IC50:  2.9000000953674316   nM  BindingDB
486IC50:  0.029999999329447746   nM  BindingDB
486IC50:  0.07000000029802322   nM  BindingDB
486IC50:  0.4000000059604645   nM  BindingDB
486IC50:  7.940000057220459   nM  BindingDB
486IC50:  3.299999952316284   nM  BindingDB
486IC50:  3.5   nM  BindingDB
486EC50:  0.30000001192092896   nM  BindingDB
486IC50:  10   nM  BindingDB
486Ki :  0.8199999928474426   nM  PDBBind
486IC50:  0.12999999523162842   nM  BindingDB
486Ki:  1   nM  BindingDB
486Ki:  15   nM  BindingDB
486EC50:  16   nM  BindingDB
486Ki:  10   nM  BindingDB
NDRKi:  1.899999976158142   nM  BindingDB
486IC50:  0.30000001192092896   nM  BindingDB
486IC50:  0.3499999940395355   nM  BindingDB
486IC50:  0.20000000298023224   nM  BindingDB
486IC50:  0.6000000238418579   nM  BindingDB
NDRKd:  0.4000000059604645   nM  BindingDB
486IC50:  0.10000000149011612   nM  BindingDB
486IC50:  0.25   nM  BindingDB
486IC50:  2.5999999046325684   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.164α = 90
b = 63.897β = 95.57
c = 70.051γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-04-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2017-12-27
    Changes: Advisory, Structure summary