4E6D

JAK2 kinase (JH1 domain) triple mutant in complex with compound 7


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.162 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Identification of Imidazo-Pyrrolopyridines as Novel and Potent JAK1 Inhibitors.

Kulagowski, J.J.Blair, W.Bull, R.J.Chang, C.Deshmukh, G.Dyke, H.J.Eigenbrot, C.Ghilardi, N.Gibbons, P.Harrison, T.K.Hewitt, P.R.Liimatta, M.Hurley, C.A.Johnson, A.Johnson, T.Kenny, J.R.Bir Kohli, P.Maxey, R.J.Mendonca, R.Mortara, K.Murray, J.Narukulla, R.Shia, S.Steffek, M.Ubhayakar, S.Ultsch, M.van Abbema, A.Ward, S.I.Waszkowycz, B.Zak, M.

(2012) J Med Chem 55: 5901-5921

  • DOI: 10.1021/jm300438j
  • Primary Citation of Related Structures:  
    4E4L, 4E4M, 4E4N, 4E6D, 4E5W, 4E6Q

  • PubMed Abstract: 
  • A therapeutic rationale is proposed for the treatment of inflammatory diseases, such as rheumatoid arthritis (RA), by specific targeting of the JAK1 pathway. Examination of the preferred binding conformation of clinically effective, pan-JAK inhibitor 1 led to identification of a novel, tricyclic hinge binding scaffold 3 ...

    A therapeutic rationale is proposed for the treatment of inflammatory diseases, such as rheumatoid arthritis (RA), by specific targeting of the JAK1 pathway. Examination of the preferred binding conformation of clinically effective, pan-JAK inhibitor 1 led to identification of a novel, tricyclic hinge binding scaffold 3. Exploration of SAR through a series of cycloamino and cycloalkylamino analogues demonstrated this template to be highly tolerant of substitution, with a predisposition to moderate selectivity for the JAK1 isoform over JAK2. This study culminated in the identification of subnanomolar JAK1 inhibitors such as 22 and 49, having excellent cell potency, good rat pharmacokinetic characteristics, and excellent kinase selectivity. Determination of the binding modes of the series in JAK1 and JAK2 by X-ray crystallography supported the design of analogues to enhance affinity and selectivity.


    Organizational Affiliation

    Department of Medicinal Chemistry, Argenta, 8/9 Spire Green Centre, Harlow CM19 5TR, United Kingdom. janusz.kulagowski@glpg



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tyrosine-protein kinase JAK2A, B298Homo sapiensMutation(s): 3 
Gene Names: JAK2
EC: 2.7.10.2
Find proteins for O60674 (Homo sapiens)
Explore O60674 
Go to UniProtKB:  O60674
NIH Common Fund Data Resources
PHAROS:  O60674
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0NU
Query on 0NU

Download Ideal Coordinates CCD File 
C [auth A], D [auth B]3-[(3R)-3-(imidazo[4,5-d]pyrrolo[2,3-b]pyridin-1(6H)-yl)piperidin-1-yl]-3-oxopropanenitrile
C16 H16 N6 O
XTKGOBBIBUQFHY-LLVKDONJSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-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 %)
0NUKi:  1.2000000476837158   nM  Binding MOAD
0NUKi:  1.2000000476837158   nM  BindingDB
0NUKi :  1.2000000476837158   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.162 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.035α = 90
b = 111.035β = 90
c = 70.575γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2012-03-15 
  • Released Date: 2012-05-30 
  • Deposition Author(s): Murray, J.M.

Revision History  (Full details and data files)

  • Version 1.0: 2012-05-30
    Type: Initial release
  • Version 1.1: 2012-07-11
    Changes: Database references