Crystal Structure of JAK1 in complex with compound 25

Experimental Data Snapshot

  • Resolution: 2.08 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 

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Identification of N-{cis-3-[Methyl(7H-pyrrolo[2,3-d]pyrimidin-4-yl)amino]cyclobutyl}propane-1-sulfonamide (PF-04965842): A Selective JAK1 Clinical Candidate for the Treatment of Autoimmune Diseases.

Vazquez, M.L.Kaila, N.Strohbach, J.W.Trzupek, J.D.Brown, M.F.Flanagan, M.E.Mitton-Fry, M.J.Johnson, T.A.TenBrink, R.E.Arnold, E.P.Basak, A.Heasley, S.E.Kwon, S.Langille, J.Parikh, M.D.Griffin, S.H.Casavant, J.M.Duclos, B.A.Fenwick, A.E.Harris, T.M.Han, S.Caspers, N.Dowty, M.E.Yang, X.Banker, M.E.Hegen, M.Symanowicz, P.T.Li, L.Wang, L.Lin, T.H.Jussif, J.Clark, J.D.Telliez, J.B.Robinson, R.P.Unwalla, R.

(2018) J Med Chem 61: 1130-1152

  • DOI: https://doi.org/10.1021/acs.jmedchem.7b01598
  • Primary Citation of Related Structures:  
    6BBU, 6BBV

  • PubMed Abstract: 

    Janus kinases (JAKs) are intracellular tyrosine kinases that mediate the signaling of numerous cytokines and growth factors involved in the regulation of immunity, inflammation, and hematopoiesis. As JAK1 pairs with JAK2, JAK3, and TYK2, a JAK1-selective inhibitor would be expected to inhibit many cytokines involved in inflammation and immune function while avoiding inhibition of the JAK2 homodimer regulating erythropoietin and thrombopoietin signaling. Our efforts began with tofacitinib, an oral JAK inhibitor approved for the treatment of rheumatoid arthritis. Through modification of the 3-aminopiperidine linker in tofacitinib, we discovered highly selective JAK1 inhibitors with nanomolar potency in a human whole blood assay. Improvements in JAK1 potency and selectivity were achieved via structural modifications suggested by X-ray crystallographic analysis. After demonstrating efficacy in a rat adjuvant-induced arthritis (rAIA) model, PF-04965842 (25) was nominated as a clinical candidate for the treatment of JAK1-mediated autoimmune diseases.

  • Organizational Affiliation

    Veterinary Medicine Research and Development, Pfizer Inc , 333 Portage Street, Kalamazoo, Michigan 49007, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase JAK1316Homo sapiensMutation(s): 0 
Gene Names: JAK1JAK1AJAK1B
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 D7D

Download Ideal Coordinates CCD File 
B [auth A]N-{cis-3-[methyl(7H-pyrrolo[2,3-d]pyrimidin-4-yl)amino]cyclobutyl}propane-1-sulfonamide
C14 H21 N5 O2 S
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on PTR
Binding Affinity Annotations 
IDSourceBinding Affinity
D7D BindingDB:  6BBU IC50: min: 5.1, max: 2511 (nM) from 9 assay(s)
Binding MOAD:  6BBU IC50: 29 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.08 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.53α = 90
b = 88.1β = 90
c = 146.05γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

  • Released Date: 2018-01-17 
  • Deposition Author(s): Han, S.

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-17
    Type: Initial release
  • Version 1.1: 2018-02-21
    Changes: Database references