JAK3 with Cyanamide CP23

Experimental Data Snapshot

  • Resolution: 1.97 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 

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Identification of Cyanamide-Based Janus Kinase 3 (JAK3) Covalent Inhibitors.

Casimiro-Garcia, A.Trujillo, J.I.Vajdos, F.Juba, B.Banker, M.E.Aulabaugh, A.Balbo, P.Bauman, J.Chrencik, J.Coe, J.W.Czerwinski, R.Dowty, M.Knafels, J.D.Kwon, S.Leung, L.Liang, S.Robinson, R.P.Telliez, J.B.Unwalla, R.Yang, X.Thorarensen, A.

(2018) J Med Chem 61: 10665-10699

  • DOI: https://doi.org/10.1021/acs.jmedchem.8b01308
  • Primary Citation of Related Structures:  
    6DA4, 6DB3, 6DB4, 6DUD

  • PubMed Abstract: 

    Ongoing interest in the discovery of selective JAK3 inhibitors led us to design novel covalent inhibitors that engage the JAK3 residue Cys909 by cyanamide, a structurally and mechanistically differentiated electrophile from other cysteine reacting groups previously incorporated in JAK3 covalent inhibitors. Through crystallography, kinetic, and computational studies, interaction of cyanamide 12 with Cys909 was optimized leading to potent and selective JAK3 inhibitors as exemplified by 32. In relevant cell-based assays and in agreement with previous results from this group, 32 demonstrated that selective inhibition of JAK3 is sufficient to drive JAK1/JAK3-mediated cellular responses. The contribution from extrahepatic processes to the clearance of cyanamide-based covalent inhibitors was also characterized using metabolic and pharmacokinetic data for 12. This work also gave key insights into a productive approach to decrease glutathione/glutathione S-transferase-mediated clearance, a challenge typically encountered during the discovery of covalent kinase inhibitors.

  • Organizational Affiliation

    Medicine Design , Pfizer Inc. , 445 Eastern Point Road , Groton , Connecticut 06340 , 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
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
G54 (Subject of Investigation/LOI)
Query on G54

Download Ideal Coordinates CCD File 
B [auth A][(1S)-1-methyl-6-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)-2,3-dihydro-1H-inden-1-yl]cyanamide
C17 H15 N5
Binding Affinity Annotations 
IDSourceBinding Affinity
G54 BindingDB:  6DB3 IC50: min: 0.7, max: 5480 (nM) from 5 assay(s)
Binding MOAD:  6DB3 IC50: 56 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.97 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.551α = 90
b = 75.557β = 90
c = 89.789γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
TRUNCATEdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

  • Released Date: 2018-11-28 
  • Deposition Author(s): Vajdos, F.F.

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-28
    Type: Initial release
  • Version 1.1: 2019-05-01
    Changes: Data collection, Database references