6GLB

Crystal structure of JAK3 in complex with Compound 20 (FM484)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.236 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Development, Optimization, and Structure-Activity Relationships of Covalent-Reversible JAK3 Inhibitors Based on a Tricyclic Imidazo[5,4- d]pyrrolo[2,3- b]pyridine Scaffold.

Forster, M.Chaikuad, A.Dimitrov, T.Doring, E.Holstein, J.Berger, B.T.Gehringer, M.Ghoreschi, K.Muller, S.Knapp, S.Laufer, S.A.

(2018) J Med Chem 61: 5350-5366

  • DOI: 10.1021/acs.jmedchem.8b00571
  • Primary Citation of Related Structures:  
    6GLB, 6GLA, 6GL9

  • PubMed Abstract: 
  • Janus kinases are major drivers of immune signaling and have been the focus of anti-inflammatory drug discovery for more than a decade. Because of the invariable colocalization of JAK1 and JAK3 at cytokine receptors, the question if selective JAK3 in ...

    Janus kinases are major drivers of immune signaling and have been the focus of anti-inflammatory drug discovery for more than a decade. Because of the invariable colocalization of JAK1 and JAK3 at cytokine receptors, the question if selective JAK3 inhibition is sufficient to effectively block downstream signaling has been highly controversial. Recently, we discovered the covalent-reversible JAK3 inhibitor FM-381 (23) featuring high isoform and kinome selectivity. Crystallography revealed that this inhibitor induces an unprecedented binding pocket by interactions of a nitrile substituent with arginine residues in JAK3. Herein, we describe detailed structure-activity relationships necessary for induction of the arginine pocket and the impact of this structural change on potency, isoform selectivity, and efficacy in cellular models. Furthermore, we evaluated the stability of this novel inhibitor class in in vitro metabolic assays and were able to demonstrate an adequate stability of key compound 23 for in vivo use.


    Organizational Affiliation

    Department of Pharmaceutical/Medicinal Chemistry , Eberhard Karls University Tübingen , Auf der Morgenstelle 8 , 72076 Tübingen , DE , Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tyrosine-protein kinase JAK3AB294Homo sapiensMutation(s): 0 
Gene Names: JAK3
EC: 2.7.10.2
Find proteins for P52333 (Homo sapiens)
Explore P52333 
Go to UniProtKB:  P52333
NIH Common Fund Data Resources
PHAROS  P52333
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
F48
Query on F48

Download CCD File 
A, B
3-[5-(3-cyclohexyl-3,5,8,10-tetrazatricyclo[7.3.0.0^{2,6}]dodeca-1(9),2(6),4,7,11-pentaen-4-yl)furan-2-yl]propanenitrile
C21 H21 N5 O
PLKGAHIHTTYWEV-UHFFFAOYSA-N
 Ligand Interaction
PHU
Query on PHU

Download CCD File 
A, B
1-phenylurea
C7 H8 N2 O
LUBJCRLGQSPQNN-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download CCD File 
A, B
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
F48IC50:  129   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.236 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.849α = 91.74
b = 50.309β = 90.28
c = 61.588γ = 92.76
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-06-27
    Type: Initial release
  • Version 1.1: 2018-07-11
    Changes: Data collection, Database references