JAK2 kinase (JH1 domain) triple mutant in complex with compound 12

Experimental Data Snapshot

  • Resolution: 1.95 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.1 of the entry. See complete history


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: https://doi.org/10.1021/jm300438j
  • Primary Citation of Related Structures:  
    4E4L, 4E4M, 4E4N, 4E5W, 4E6D, 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. 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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase JAK2
A, B
298Homo sapiensMutation(s): 3 
Gene Names: JAK2
UniProt & NIH Common Fund Data Resources
Find proteins for O60674 (Homo sapiens)
Explore O60674 
Go to UniProtKB:  O60674
PHAROS:  O60674
GTEx:  ENSG00000096968 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60674
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 0NV

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C20 H21 N5
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on PTR
A, B
Binding Affinity Annotations 
IDSourceBinding Affinity
0NV Binding MOAD:  4E6Q Ki: 4.4 (nM) from 1 assay(s)
PDBBind:  4E6Q Ki: 4.4 (nM) from 1 assay(s)
BindingDB:  4E6Q Ki: 4.4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.95 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.189 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.502α = 90
b = 103.854β = 90.02
c = 69.999γ = 90
Software Package:
Software NamePurpose
d*TREKdata scaling
SCALAdata scaling
PDB_EXTRACTdata extraction
CBASSdata collection
d*TREKdata reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

  • 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