1SQN

Progesterone Receptor Ligand Binding Domain with bound Norethindrone


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Progesterone receptor ligand binding pocket flexibility: crystal structures of the norethindrone and mometasone furoate complexes

Madauss, K.P.Deng, J.-S.Austin, R.J.H.Lambert, M.H.McLay, I.Pritchard, J.Short, S.A.Stewart, E.L.Uings, I.J.Williams, S.P.

(2004) J Med Chem 47: 3381-3387

  • DOI: 10.1021/jm030640n
  • Primary Citation of Related Structures:  
    1SQN, 1SR7

  • PubMed Abstract: 
  • Although progesterone, the natural ligand of the progesterone receptor (PR), has a hydrogen atom at the 17alpha position, other potent steroid agonists such as norethindrone and mometasone furoate have larger substituents at this position that are accommodated by the PR ligand binding pocket ...

    Although progesterone, the natural ligand of the progesterone receptor (PR), has a hydrogen atom at the 17alpha position, other potent steroid agonists such as norethindrone and mometasone furoate have larger substituents at this position that are accommodated by the PR ligand binding pocket. Crystallographic analysis of PR ligand binding domain complexes clearly demonstrated that these moieties were accommodated by local shifts of the protein main chain and by adoption of alternative side chain rotamer conformations of ligand-proximal amino acids. These conformational changes imparted a ligand-specific volume to the binding pocket, from 490 A3 in the metribolone complex to 520 A3 in the norethindrone complex, 565 A3 in the progesterone complex, and 730 A3 in the mometasone furoate complex. Despite these marked alterations in binding pocket volume, critical interactions essential for establishment of an active AF2 conformation were maintained.


    Organizational Affiliation

    GlaxoSmithKline Inc., 5 Moore Drive, Research Triangle Park, North Carolina 27709, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
progesterone receptorA, B261Homo sapiensMutation(s): 0 
Gene Names: HUMPGRRPGRNR3C3
UniProt & NIH Common Fund Data Resources
Find proteins for P06401 (Homo sapiens)
Explore P06401 
Go to UniProtKB:  P06401
PHAROS:  P06401
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NDR
Query on NDR

Download Ideal Coordinates CCD File 
C [auth A], D [auth B](14beta,17alpha)-17-ethynyl-17-hydroxyestr-4-en-3-one
C20 H26 O2
VIKNJXKGJWUCNN-XGXHKTLJSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NDREC50:  2.200000047683716   nM  BindingDB
NDRKi:  1.899999976158142   nM  BindingDB
NDRIC50:  3.200000047683716   nM  BindingDB
NDRKd :  0.4000000059604645   nM  PDBBind
NDRKd:  0.4000000059604645   nM  BindingDB
NDRKd:  0.4000000059604645   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.753α = 90
b = 64.142β = 95.84
c = 70.138γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-07-27
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-01-31
    Changes: Experimental preparation