6EL6

Glucocorticoid Receptor in complex with compound 4

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.252 

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Literature

Discovery of a Novel Oral Glucocorticoid Receptor Modulator (AZD9567) with Improved Side Effect Profile.

Ripa, L., Edman, K., Dearman, M., Edenro, G., Hendrickx, R., Ullah, V., Chang, H.F., Lepisto, M., Chapman, D., Geschwindner, S., Wissler, L., Svanberg, P., Lawitz, K., Malmberg, J., Nikitidis, A., Olsson, R.I., Bird, J., Llinas, A., Hegelund-Myrback, T., Berger, M., Thorne, P., Harrison, R., Kohler, C., Drmota, T.

(2018) J Med Chem 61: 1785-1799

  • DOI: 10.1021/acs.jmedchem.7b01690
  • Primary Citation of Related Structures:  
    6EL6, 6EL7, 6EL9

  • PubMed Abstract: 

    • Synthetic glucocorticoids (GC) are essential for the treatment of a broad range of inflammatory diseases. However, their use is limited by target related adverse effects on, e.g., glucose homeostasis and bone metabolism. Starting from a nonsteroidal GR ligand (4) that is a full agonist in reporter gene assays, we exploited key functional triggers within the receptor, generating a range of structurally diverse partial agonists ...

    Synthetic glucocorticoids (GC) are essential for the treatment of a broad range of inflammatory diseases. However, their use is limited by target related adverse effects on, e.g., glucose homeostasis and bone metabolism. Starting from a nonsteroidal GR ligand (4) that is a full agonist in reporter gene assays, we exploited key functional triggers within the receptor, generating a range of structurally diverse partial agonists. Of these, only a narrow subset exhibited full anti-inflammatory efficacy and a significantly reduced impact on adverse effect markers in human cell assays compared to prednisolone. This led to the discovery of AZD9567 (15) with excellent in vivo efficacy when dosed orally in a rat model of joint inflammation. Compound 15 is currently being evaluated in clinical trials comparing the efficacy and side effect markers with those of prednisolone.

    Organizational Affiliation: 

    Respiratory, Inflammation and Autoimmunity, IMED Biotech Unit , AstraZeneca Gothenburg , Pepparedsleden 1 , Mölndal 43183 , Sweden.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glucocorticoid receptorA280Homo sapiensMutation(s): 4 
Gene Names: NR3C1, GRL
UniProt & NIH Common Fund Data Resources
Find proteins for P04150 (Homo sapiens)
Explore P04150 
Go to UniProtKB:  P04150
PHAROS:  P04150
GTEx:  ENSG00000113580 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04150
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear receptor coactivator 2B14Homo sapiensMutation(s): 0 
Gene Names: NCOA2, BHLHE75, SRC2, TIF2
UniProt & NIH Common Fund Data Resources
Find proteins for Q15596 (Homo sapiens)
Explore Q15596 
Go to UniProtKB:  Q15596
PHAROS:  Q15596
GTEx:  ENSG00000140396 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15596
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
B9Q
Query on B9Q
Download Ideal Coordinates CCD File 
D [auth A]~{N}-[(1~{R},2~{S})-1-[1-(4-fluorophenyl)indazol-5-yl]oxy-1-(6-methoxypyridin-3-yl)propan-2-yl]cyclopropanecarboxamide
C26 H25 F N4 O3
YDRQCGICZKAGCQ-LMKMVOKYSA-N		 Ligand Interaction
EDO
Query on EDO
Download Ideal Coordinates CCD File 
C [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
B9Q BindingDB:  6EL6 IC50: min: 0.24, max: 46 (nM) from 5 assay(s)
EC50: 1.3 (nM) from 1 assay(s)
Binding MOAD:  6EL6 IC50: 6.3 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.252 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.955α = 90
b = 84.955β = 90
c = 106.374γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

  • Deposited Date: 2017-09-28 
  • Released Date: 2018-02-21 
    • Deposition Author(s): Edman, K., Wissler, L.

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-21
    Type: Initial release
  • Version 1.1: 2018-03-21
    Changes: Database references