3K22

Glucocorticoid Receptor with Bound alaninamide 10 with TIF2 peptide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

Design and x-ray crystal structures of high-potency nonsteroidal glucocorticoid agonists exploiting a novel binding site on the receptor.

Biggadike, K., Bledsoe, R.K., Coe, D.M., Cooper, T.W., House, D., Iannone, M.A., Macdonald, S.J., Madauss, K.P., McLay, I.M., Shipley, T.J., Taylor, S.J., Tran, T.B., Uings, I.J., Weller, V., Williams, S.P.

(2009) Proc.Natl.Acad.Sci.USA 106: 18114-18119

  • DOI: 10.1073/pnas.0909125106
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Crystallography and computer modeling have been used to exploit a previously unexplored channel in the glucocorticoid receptor (GR). Highly potent, nonsteroidal indazole amides showing excellent complementarity to the channel were designed with the a ...

    Crystallography and computer modeling have been used to exploit a previously unexplored channel in the glucocorticoid receptor (GR). Highly potent, nonsteroidal indazole amides showing excellent complementarity to the channel were designed with the assistance of the computational technique AlleGrow. The accuracy of the design process was demonstrated through crystallographic structural determination of the GR ligand-binding domain-agonist complex of the D-prolinamide derivative 11. The utility of the channel was further exemplified through the design of a potent phenylindazole in which structural motifs, seen to interact with the traditional GR ligand pocket, were abandoned and replaced by interactions within the new channel. Occupation of the channel was confirmed with a second GR crystal structure of this truncated D-alaninamide derivative 13. Compound 11 displays properties compatible with development as an intranasal solution formulation, whereas oral bioavailability has been demonstrated with a related truncated exemplar 14. Data with the pyrrolidinone amide 12 demonstrate the potential for further elaboration within the "meta" channel to deliver compounds with selectivity for the desired transrepressive activity of glucocorticoids. The discovery of these interactions with this important receptor offers significant opportunities for the design of novel GR modulators.

    Organizational Affiliation: 

    Medicinal Chemistry, Respiratory Center of Excellence for Drug Discovery, GlaxoSmithKline Medicines Research Center, Stevenage, Hertfordshire SG1 2NY, United Kingdom. keith.b.biggadike@gsk.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glucocorticoid receptor
A, B
259Homo sapiensMutation(s): 2 
Gene Names: NR3C1 (GRL)
Find proteins for P04150 (Homo sapiens)
Go to Gene View: NR3C1
Go to UniProtKB:  P04150
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Transcriptional Intermediary Factor 2
H, D
12Homo sapiensMutation(s): 0 
Gene Names: NCOA2 (BHLHE75, SRC2, TIF2)
Find proteins for Q15596 (Homo sapiens)
Go to Gene View: NCOA2
Go to UniProtKB:  Q15596
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JZR
Query on JZR
Download SDF File 
Download CCD File 
A, B
hexyl beta-D-glucopyranoside
C12 H24 O6
JVAZJLFFSJARQM-RMPHRYRLSA-N
 Ligand Interaction
JZS
Query on JZS
Download SDF File 
Download CCD File 
A, B
N-[(1R)-2-amino-1-methyl-2-oxoethyl]-3-(6-methyl-4-{[3,3,3-trifluoro-2-hydroxy-2-(trifluoromethyl)propyl]amino}-1H-indazol-1-yl)benzamide
C22 H21 F6 N5 O3
SDBGIXABAWIVLY-GFCCVEGCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
JZSIC50: 12.59 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.211 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 127.597α = 90.00
b = 127.597β = 90.00
c = 78.230γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-08-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2013-09-25
    Type: Derived calculations
  • Version 1.3: 2017-11-01
    Type: Refinement description