3E7C

Glucocorticoid Receptor LBD bound to GSK866


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.210 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The first X-ray crystal structure of the glucocorticoid receptor bound to a non-steroidal agonist.

Madauss, K.P.Bledsoe, R.K.Mclay, I.Stewart, E.L.Uings, I.J.Weingarten, G.Williams, S.P.

(2008) Bioorg Med Chem Lett 18: 6097-6099

  • DOI: 10.1016/j.bmcl.2008.10.021
  • Primary Citation of Related Structures:  
    3E7C

  • PubMed Abstract: 
  • The amino-pyrazole 2,6-dichloro-N-ethyl benzamide 1 is a selective GR agonist with dexamethasone-like in vitro potency. Its X-ray crystal structure in the GR LBD (Glucocorticoid ligand-binding domain) is described and compared to other reported structures of steroidal GR agonists in the GR LBD (3E7C) ...

    The amino-pyrazole 2,6-dichloro-N-ethyl benzamide 1 is a selective GR agonist with dexamethasone-like in vitro potency. Its X-ray crystal structure in the GR LBD (Glucocorticoid ligand-binding domain) is described and compared to other reported structures of steroidal GR agonists in the GR LBD (3E7C).


    Organizational Affiliation

    Department of Computational and Structural Chemistry, Molecular Discovery Research, GlaxoSmithKline, 5 Moore Drive, Research Triangle Park, NC 27709, USA. kevin.p.madauss@gsk.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glucocorticoid receptor AB257Homo sapiensMutation(s): 2 
Gene Names: NR3C1GRL
Find proteins for P04150 (Homo sapiens)
Explore P04150 
Go to UniProtKB:  P04150
NIH Common Fund Data Resources
PHAROS:  P04150
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear receptor coactivator 2 DH11Homo sapiensMutation(s): 0 
Gene Names: NCOA2BHLHE75SRC2TIF2
Find proteins for Q15596 (Homo sapiens)
Explore Q15596 
Go to UniProtKB:  Q15596
NIH Common Fund Data Resources
PHAROS:  Q15596
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
866
Query on 866

Download Ideal Coordinates CCD File 
A, B
5-amino-N-[(2S)-2-({[(2,6-dichlorophenyl)carbonyl](ethyl)amino}methyl)-3,3,3-trifluoro-2-hydroxypropyl]-1-(4-fluorophenyl)-1H-pyrazole-4-carboxamide
C23 H21 Cl2 F4 N5 O3
LKQMULLPLYLIGW-QFIPXVFZSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
A, B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
866EC50:  2   nM  BindingDB
866IC50:  3.1600000858306885   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.210 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.654α = 90
b = 126.654β = 90
c = 78.991γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
StructureStudiodata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-11-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2014-04-02
    Changes: Source and taxonomy
  • Version 1.3: 2017-10-25
    Changes: Refinement description