3FUP

Crystal structures of JAK1 and JAK2 inhibitor complexes


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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: 10.1016/j.jmb.2009.01.041
  • Structures With Same Primary Citation

  • 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 dis ...

    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.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tyrosine-protein kinase JAK2A, B293Homo sapiensMutation(s): 1 
Gene Names: JAK2jak2 (amino acids 843 - 1132)
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
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MI1
Query on MI1

Download CCD File 
A, B
3-{(3R,4R)-4-methyl-3-[methyl(7H-pyrrolo[2,3-d]pyrimidin-4-yl)amino]piperidin-1-yl}-3-oxopropanenitrile
C16 H20 N6 O
UJLAWZDWDVHWOW-YPMHNXCESA-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 %)
MI1IC50:  2.5   nM  BindingDB
MI1IC50:  682   nM  BindingDB
MI1IC50:  740   nM  BindingDB
MI1IC50:  3.0999999046325684   nM  BindingDB
MI1IC50:  4   nM  BindingDB
MI1IC50:  71   nM  BindingDB
MI1Kd:  5   nM  BindingDB
MI1EC50:  184   nM  BindingDB
MI1IC50:  72   nM  BindingDB
MI1IC50:  75   nM  BindingDB
MI1IC50:  77   nM  BindingDB
MI1IC50:  0.6000000238418579   nM  BindingDB
MI1IC50:  1.399999976158142   nM  BindingDB
MI1IC50:  1377   nM  BindingDB
MI1IC50:  95   nM  BindingDB
MI1IC50:  107   nM  BindingDB
MI1IC50:  21.700000762939453   nM  Binding MOAD
MI1IC50:  155   nM  BindingDB
MI1IC50:  2.799999952316284   nM  BindingDB
MI1IC50:  170   nM  BindingDB
MI1IC50:  11   nM  BindingDB
MI1Kd:  1.7999999523162842   nM  BindingDB
MI1IC50:  184   nM  BindingDB
MI1IC50:  190   nM  BindingDB
MI1IC50:  2.200000047683716   nM  BindingDB
MI1IC50:  12   nM  BindingDB
MI1IC50:  4.099999904632568   nM  BindingDB
MI1Ki:  5000   nM  BindingDB
MI1IC50:  229   nM  BindingDB
MI1IC50 :  21.700000762939453   nM  PDBBind
MI1IC50:  1.600000023841858   nM  BindingDB
MI1IC50:  265   nM  BindingDB
MI1IC50:  275   nM  BindingDB
MI1IC50:  302   nM  BindingDB
MI1Ki:  0.9900000095367432   nM  BindingDB
MI1IC50:  20   nM  BindingDB
MI1IC50:  409   nM  BindingDB
MI1EC50:  93   nM  BindingDB
MI1Ki:  0.699999988079071   nM  BindingDB
MI1Kd:  0.5799999833106995   nM  BindingDB
MI1IC50:  30   nM  BindingDB
MI1IC50:  33   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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