Crystal structures of JAK1 and JAK2 inhibitor complexes

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.182 

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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 kinase JAK2
A, B
293Homo sapiensMutation(s): 1 
Gene Names: JAK2jak2 (amino acids 843 - 1132)
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 MI1

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C16 H20 N6 O
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on PTR
A, B
Binding Affinity Annotations 
IDSourceBinding Affinity
MI1 BindingDB:  3FUP Ki: min: 0.7, max: 5000 (nM) from 3 assay(s)
Kd: min: 0.58, max: 5 (nM) from 3 assay(s)
IC50: min: 0.5, max: 4724 (nM) from 58 assay(s)
EC50: min: 93, max: 184 (nM) from 2 assay(s)
Binding MOAD:  3FUP IC50: 21.7 (nM) from 1 assay(s)
PDBBind:  3FUP IC50: 21.7 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.182 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.491α = 90
b = 110.491β = 90
c = 70.317γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-02-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2020-02-26
    Changes: Data collection, Derived calculations
  • Version 1.3: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-09-06
    Changes: Data collection, Refinement description
  • Version 1.5: 2023-11-22
    Changes: Data collection