Jak3 with covalent inhibitor 6

Experimental Data Snapshot

  • Resolution: 1.93 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 

wwPDB Validation   3D Report Full Report

This is version 1.1 of the entry. See complete history


Design of a Janus Kinase 3 (JAK3) Specific Inhibitor 1-((2S,5R)-5-((7H-Pyrrolo[2,3-d]pyrimidin-4-yl)amino)-2-methylpiperidin-1-yl)prop-2-en-1-one (PF-06651600) Allowing for the Interrogation of JAK3 Signaling in Humans.

Thorarensen, A.Dowty, M.E.Banker, M.E.Juba, B.Jussif, J.Lin, T.Vincent, F.Czerwinski, R.M.Casimiro-Garcia, A.Unwalla, R.Trujillo, J.I.Liang, S.Balbo, P.Che, Y.Gilbert, A.M.Brown, M.F.Hayward, M.Montgomery, J.Leung, L.Yang, X.Soucy, S.Hegen, M.Coe, J.Langille, J.Vajdos, F.Chrencik, J.Telliez, J.B.

(2017) J Med Chem 60: 1971-1993

  • DOI: https://doi.org/10.1021/acs.jmedchem.6b01694
  • Primary Citation of Related Structures:  
    5TTS, 5TTU, 5TTV

  • PubMed Abstract: 

    Significant work has been dedicated to the discovery of JAK kinase inhibitors resulting in several compounds entering clinical development and two FDA approved NMEs. However, despite significant effort during the past 2 decades, identification of highly selective JAK3 inhibitors has eluded the scientific community. A significant effort within our research organization has resulted in the identification of the first orally active JAK3 specific inhibitor, which achieves JAK isoform specificity through covalent interaction with a unique JAK3 residue Cys-909. The relatively rapid resynthesis rate of the JAK3 enzyme presented a unique challenge in the design of covalent inhibitors with appropriate pharmacodynamics properties coupled with limited unwanted off-target reactivity. This effort resulted in the identification of 11 (PF-06651600), a potent and low clearance compound with demonstrated in vivo efficacy. The favorable efficacy and safety profile of this JAK3-specific inhibitor 11 led to its evaluation in several human clinical studies.

  • Organizational Affiliation

    Pharmacokinetics, Dynamics, and Metabolism, Pfizer Worldwide R&D , 1 Burtt Road, Andover, Massachusetts 01810, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase JAK3321Homo sapiensMutation(s): 1 
Gene Names: JAK3
UniProt & NIH Common Fund Data Resources
Find proteins for P52333 (Homo sapiens)
Explore P52333 
Go to UniProtKB:  P52333
PHAROS:  P52333
GTEx:  ENSG00000105639 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP52333
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 7KX

Download Ideal Coordinates CCD File 
B [auth A]N-[3-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)phenyl]propanamide
C15 H14 N4 O
Experimental Data & Validation

Experimental Data

  • Resolution: 1.93 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.628α = 90
b = 75.661β = 90
c = 88.74γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
DENZOdata reduction

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

  • Released Date: 2017-02-22 
  • Deposition Author(s): Vajdos, F.F.

Revision History  (Full details and data files)

  • Version 1.0: 2017-02-22
    Type: Initial release
  • Version 1.1: 2017-03-22
    Changes: Database references