4EI4

JAK1 kinase (JH1 domain) in complex with compound 20


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Discovery and optimization of C-2 methyl imidazopyrrolopyridines as potent and orally bioavailable JAK1 inhibitors with selectivity over JAK2.

Zak, M.Mendonca, R.Balazs, M.Barrett, K.Bergeron, P.Blair, W.S.Chang, C.Deshmukh, G.Devoss, J.Dragovich, P.S.Eigenbrot, C.Ghilardi, N.Gibbons, P.Gradl, S.Hamman, C.Hanan, E.J.Harstad, E.Hewitt, P.R.Hurley, C.A.Jin, T.Johnson, A.Johnson, T.Kenny, J.R.Koehler, M.F.Bir Kohli, P.Kulagowski, J.J.Labadie, S.Liao, J.Liimatta, M.Lin, Z.Lupardus, P.J.Maxey, R.J.Murray, J.M.Pulk, R.Rodriguez, M.Savage, S.Shia, S.Steffek, M.Ubhayakar, S.Ultsch, M.van Abbema, A.Ward, S.I.Xiao, L.Xiao, Y.

(2012) J.Med.Chem. 55: 6176-6193

  • DOI: 10.1021/jm300628c
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Herein we report the discovery of the C-2 methyl substituted imidazopyrrolopyridine series and its optimization to provide potent and orally bioavailable JAK1 inhibitors with selectivity over JAK2. The C-2 methyl substituted inhibitor 4 exhibited not ...

    Herein we report the discovery of the C-2 methyl substituted imidazopyrrolopyridine series and its optimization to provide potent and orally bioavailable JAK1 inhibitors with selectivity over JAK2. The C-2 methyl substituted inhibitor 4 exhibited not only improved JAK1 potency relative to unsubstituted compound 3 but also notable JAK1 vs JAK2 selectivity (20-fold and >33-fold in biochemical and cell-based assays, respectively). Features of the X-ray structures of 4 in complex with both JAK1 and JAK2 are delineated. Efforts to improve the in vitro and in vivo ADME properties of 4 while maintaining JAK1 selectivity are described, culminating in the discovery of a highly optimized and balanced inhibitor (20). Details of the biological characterization of 20 are disclosed including JAK1 vs JAK2 selectivity levels, preclinical in vivo PK profiles, performance in an in vivo JAK1-mediated PK/PD model, and attributes of an X-ray structure in complex with JAK1.


    Organizational Affiliation

    Department of Discovery Chemistry, Genentech, Inc, South San Francisco, CA 94080, USA. mzak@gene.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tyrosine-protein kinase JAK1
A, B
302Homo sapiensMutation(s): 0 
Gene Names: JAK1 (JAK1A, JAK1B)
EC: 2.7.10.2
Find proteins for P23458 (Homo sapiens)
Go to Gene View: JAK1
Go to UniProtKB:  P23458
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0Q2
Query on 0Q2

Download SDF File 
Download CCD File 
A, B
(1R,3R)-3-(2-methylimidazo[4,5-d]pyrrolo[2,3-b]pyridin-1(8H)-yl)cyclohexanol
C15 H18 N4 O
IWJKSSOUXRKEPE-GHMZBOCLSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR
A, B
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0Q2Ki: 1.8 nM BINDINGMOAD
0Q2Ki: 1.8 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.200 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 42.755α = 90.00
b = 173.322β = 94.27
c = 44.595γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
SCALEPACKdata scaling
Blu-Icedata collection
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-07-04
    Type: Initial release
  • Version 1.1: 2013-01-02
    Type: Database references
  • Version 1.2: 2013-01-23
    Type: Database references
  • Version 1.3: 2017-11-15
    Type: Refinement description