Crystal structures of JAK1 and JAK2 inhibitor complexes

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.178 

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Dissecting specificity in the Janus kinases: the structures of JAK-specific inhibitors complexed to the JAK1 and JAK2 protein tyrosine kinase domains.

Williams, N.K.Bamert, R.S.Patel, O.Wang, C.Walden, P.M.Wilks, A.F.Fantino, E.Rossjohn, J.Lucet, I.S.

(2009) J Mol Biol 387: 219-232

  • DOI: https://doi.org/10.1016/j.jmb.2009.01.041
  • Primary Citation of Related Structures:  
    3EYG, 3EYH, 3FUP

  • PubMed Abstract: 

    The Janus kinases (JAKs) are a pivotal family of protein tyrosine kinases (PTKs) that play prominent roles in numerous cytokine signaling pathways, with aberrant JAK activity associated with a variety of hematopoietic malignancies, cardiovascular diseases and immune-related disorders. Whereas the structures of the JAK2 and JAK3 PTK domains have been determined, the structure of the JAK1 PTK domain is unknown. Here, we report the high-resolution crystal structures of the "active form" of the JAK1 PTK domain in complex with two JAK inhibitors, a tetracyclic pyridone 2-t-butyl-9-fluoro-3,6-dihydro-7H-benz[h]-imidaz[4,5-f]isoquinoline-7-one (CMP6) and (3R,4R)-3-[4-methyl-3-[N-methyl-N-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)amino]piperidin-1-yl]-3-oxopropionitrile (CP-690,550), and compare them with the corresponding JAK2 PTK inhibitor complexes. Both inhibitors bound in a similar manner to JAK1, namely buried deep within a constricted ATP-binding site, thereby providing a basis for the potent inhibition of JAK1. As expected, the mode of inhibitor binding in JAK1 was very similar to that observed in JAK2, highlighting the challenges in developing JAK-specific inhibitors that target the ATP-binding site. Nevertheless, differences surrounding the JAK1 and JAK2 ATP-binding sites were apparent, thereby providing a platform for the rational design of JAK2- and JAK1-specific inhibitors.

  • Organizational Affiliation

    Protein Crystallography Unit, Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria, Australia.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase290Homo sapiensMutation(s): 0 
Gene Names: JAK1hCG_22179
UniProt & NIH Common Fund Data Resources
Find proteins for P23458 (Homo sapiens)
Explore P23458 
Go to UniProtKB:  P23458
PHAROS:  P23458
GTEx:  ENSG00000162434 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23458
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on IZA

Download Ideal Coordinates CCD File 
C18 H16 F N3 O
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on PTR
Binding Affinity Annotations 
IDSourceBinding Affinity
IZA BindingDB:  3EYH IC50: min: 4, max: 600 (nM) from 4 assay(s)
PDBBind:  3EYH IC50: 20 (nM) from 1 assay(s)
Binding MOAD:  3EYH IC50: 20 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.178 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45α = 90
b = 88.22β = 90
c = 145.52γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-02-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-12-27
    Changes: Data collection, Database references, Derived calculations