4LSJ

Crystal Structure of the Glucocorticoid Receptor Ligand Binding Domain Bound to a Dibenzoxapine Sulfonamide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.185 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Glucocorticoid receptor modulators informed by crystallography lead to a new rationale for receptor selectivity, function, and implications for structure-based design.

Carson, M.W., Luz, J.G., Suen, C., Montrose, C., Zink, R., Ruan, X., Cheng, C., Cole, H., Adrian, M.D., Kohlman, D.T., Mabry, T., Snyder, N., Condon, B., Maletic, M., Clawson, D., Pustilnik, A., Coghlan, M.J.

(2014) J Med Chem 57: 849-860

  • DOI: 10.1021/jm401616g
  • Primary Citation of Related Structures:  
    4LSJ

  • PubMed Abstract: 

    • The structural basis of the pharmacology enabling the use of glucocorticoids as reliable treatments for inflammation and autoimmune diseases has been augmented with a new group of glucocorticoid receptor (GR) ligands. Compound 10, the archetype of a new family of dibenzoxepane and dibenzosuberane sulfonamides, is a potent anti-inflammatory agent with selectivity for the GR versus other steroid receptors and a differentiated gene expression profile versus clinical glucocorticoids (lower GR transactivation with comparable transrepression) ...

    The structural basis of the pharmacology enabling the use of glucocorticoids as reliable treatments for inflammation and autoimmune diseases has been augmented with a new group of glucocorticoid receptor (GR) ligands. Compound 10, the archetype of a new family of dibenzoxepane and dibenzosuberane sulfonamides, is a potent anti-inflammatory agent with selectivity for the GR versus other steroid receptors and a differentiated gene expression profile versus clinical glucocorticoids (lower GR transactivation with comparable transrepression). A stereospecific synthesis of this chiral molecule provides the unique topology needed for biological activity and structural biology. In vivo activity of 10 in acute and chronic models of inflammation is equivalent to prednisolone. The crystal structure of compound 10 within the GR ligand binding domain (LBD) unveils a novel binding conformation distinct from the classic model adopted by cognate ligands. The overall conformation of the GR LBD/10 complex provides a new basis for binding, selectivity, and anti-inflammatory activity and a path for further insights into structure-based ligand design.

    Organizational Affiliation: 

    Lilly Research Laboratories, A Division of Eli Lilly & Co., Lilly Corporate Center, Indianapolis, Indiana 46285, United States.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glucocorticoid receptor A258Homo sapiensMutation(s): 2 
Gene Names: NR3C1, GRL
Find proteins for P04150 (Homo sapiens)
Explore P04150 
Go to UniProtKB:  P04150
NIH Common Fund Data Resources
PHAROS:  P04150
GTEx:  ENSG00000113580
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
D30 peptide B13N/AMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LSJ
Query on LSJ
Download Ideal Coordinates CCD File 
A
N-{3-[(1Z)-1-(10-methoxydibenzo[b,e]oxepin-11(6H)-ylidene)propyl]phenyl}methanesulfonamide
C25 H25 N O4 S
PHIKAOOZNGLKDI-QQTULTPQSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
LSJIC50:  4.380000114440918   nM  Binding MOAD
LSJKi:  0.27000001072883606   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.185 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.962α = 90
b = 139.398β = 90
c = 48.068γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
d*TREKdata reduction
d*TREKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-01-29
    Type: Initial release
  • Version 1.1: 2014-03-12
    Changes: Database references