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 
  • R-Value Observed: 0.202 

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:  
    4F08, 4F09, 4EI4, 4EHZ

  • 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 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) ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tyrosine-protein kinase JAK1 AB302Homo sapiensMutation(s): 0 
Gene Names: JAK1JAK1AJAK1B
EC: 2.7.10.2
Find proteins for P23458 (Homo sapiens)
Explore P23458 
Go to UniProtKB:  P23458
NIH Common Fund Data Resources
PHAROS:  P23458
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0Q2
Query on 0Q2

Download Ideal Coordinates 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,BL-PEPTIDE LINKINGC9 H12 N O6 PTYR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0Q2Ki:  1.7999999523162842   nM  Binding MOAD
0Q2Ki :  1.7999999523162842   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 
  • R-Value Observed: 0.202 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.755α = 90
b = 173.322β = 94.27
c = 44.595γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

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