4IVC

JAK1 kinase (JH1 domain) in complex with the inhibitor (TRANS-4-{2-[(1R)-1-HYDROXYETHYL]IMIDAZO[4,5-D]PYRROLO[2,3-B]PYRIDIN-1(6H)-YL}CYCLOHEXYL)ACETONITRILE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Identification of C-2 Hydroxyethyl Imidazopyrrolopyridines as Potent JAK1 Inhibitors with Favorable Physicochemical Properties and High Selectivity over JAK2.

Zak, M.Hurley, C.A.Ward, S.I.Bergeron, P.Barrett, K.Balazs, M.Blair, W.S.Bull, R.Chakravarty, P.Chang, C.Crackett, P.Deshmukh, G.Devoss, J.Dragovich, P.S.Eigenbrot, C.Ellwood, C.Gaines, S.Ghilardi, N.Gibbons, P.Gradl, S.Gribling, P.Hamman, C.Harstad, E.Hewitt, P.Johnson, A.Johnson, T.Kenny, J.R.Koehler, M.F.Bir Kohli, P.Labadie, S.Lee, W.P.Liao, J.Liimatta, M.Mendonca, R.Narukulla, R.Pulk, R.Reeve, A.Savage, S.Shia, S.Steffek, M.Ubhayakar, S.van Abbema, A.Aliagas, I.Avitabile-Woo, B.Xiao, Y.Yang, J.Kulagowski, J.J.

(2013) J.Med.Chem. 56: 4764-4785

  • DOI: 10.1021/jm4004895
  • Primary Citation of Related Structures:  4IVA, 4IVB, 4IVD

  • PubMed Abstract: 
  • Herein we report on the structure-based discovery of a C-2 hydroxyethyl moiety which provided consistently high levels of selectivity for JAK1 over JAK2 to the imidazopyrrolopyridine series of JAK1 inhibitors. X-ray structures of a C-2 hydroxyethyl a ...

    Herein we report on the structure-based discovery of a C-2 hydroxyethyl moiety which provided consistently high levels of selectivity for JAK1 over JAK2 to the imidazopyrrolopyridine series of JAK1 inhibitors. X-ray structures of a C-2 hydroxyethyl analogue in complex with both JAK1 and JAK2 revealed differential ligand/protein interactions between the two isoforms and offered an explanation for the observed selectivity. Analysis of historical data from related molecules was used to develop a set of physicochemical compound design parameters to impart desirable properties such as acceptable membrane permeability, potent whole blood activity, and a high degree of metabolic stability. This work culminated in the identification of a highly JAK1 selective compound (31) exhibiting favorable oral bioavailability across a range of preclinical species and robust efficacy in a rat CIA model.


    Organizational Affiliation

    Department of Discovery Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, USA. mzak@gene.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tyrosine-protein kinase JAK1
A, B
302Homo sapiensGene 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
1J6
Query on 1J6

Download SDF File 
Download CCD File 
A, B
(trans-4-{2-[(1R)-1-hydroxyethyl]imidazo[4,5-d]pyrrolo[2,3-b]pyridin-1(6H)-yl}cyclohexyl)acetonitrile
C18 H21 N5 O
IKSRDHMMQOCRHN-JHJVBQTASA-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 %)
1J6Ki: 0.1 nM (100) BINDINGDB
1J6EC50: 5.7 - 28 nM (100) BINDINGDB
1J6Ki: 0.1 nM BINDINGMOAD
1J6Ki: 0.1 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.197 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 42.329α = 90.00
b = 172.868β = 94.75
c = 44.124γ = 90.00
Software Package:
Software NamePurpose
MAR345dtbdata collection
HKL-2000data reduction
SCALEPACKdata scaling
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-05-22
    Type: Initial release
  • Version 1.1: 2013-07-03
    Type: Database references