5G3J

Discovery of New Selective Glucocorticoid Receptor Agonist Leads


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Discovery of New Selective Glucocorticoid Receptor Agonist Leads.

Berger, M.Rehwinkel, H.Schmees, N.Schacke, H.Edman, K.Wissler, L.Reichel, A.Jaroch, S.

(2017) Bioorg Med Chem Lett 27: 437

  • DOI: 10.1016/j.bmcl.2016.12.047
  • Primary Citation of Related Structures:  
    5G3J

  • PubMed Abstract: 
  • We report on the discovery of two new lead series for the development of glucocorticoid receptor agonists. Firstly, the discovery of tetrahydronaphthalenes led to metabolically stable and dissociated compounds. Their binding mode to the glucocorticoid re ...

    We report on the discovery of two new lead series for the development of glucocorticoid receptor agonists. Firstly, the discovery of tetrahydronaphthalenes led to metabolically stable and dissociated compounds. Their binding mode to the glucocorticoid receptor could be elucidated through an X-ray structure. Closer inspection into the reaction path and analyses of side products revealed a new amino alcohol series also addressing the glucocorticoid receptor and demonstrating strong anti-inflammatory activity in vitro.


    Organizational Affiliation

    Global External Innovation & Alliances, Candidate Generation & External Innovation, Drug Discovery, Bayer Pharma AG, D-13353 Berlin, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GLUCOCORTICOID RECEPTOR A280Homo sapiensMutation(s): 4 
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 B14Homo 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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CPS
Query on CPS

Download Ideal Coordinates CCD File 
A
3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE
C32 H58 N2 O7 S
UMCMPZBLKLEWAF-BCTGSCMUSA-N
 Ligand Interaction
E7T
Query on E7T

Download Ideal Coordinates CCD File 
A
5-[[(1S,2R,4R)-4-ethyl-6,7-bis(fluoranyl)-2,5-bis(oxidanyl)-2-(trifluoromethyl)-3,4-dihydro-1H-naphthalen-1-yl]amino]-1H-quinolin-2-one
C22 H19 F5 N2 O3
VZPLUSXTJULLCS-SYQZRHMFSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
E7TIC50:  63   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.263α = 90
b = 84.263β = 90
c = 106.678γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-02-15
    Type: Initial release
  • Version 1.1: 2017-08-23
    Changes: Data collection
  • Version 1.2: 2019-04-03
    Changes: Data collection, Source and taxonomy