6DB4

JAK3 with Cyanamide CP34


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

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

  • 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 gr ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tyrosine-protein kinase JAK3A321Homo sapiensMutation(s): 1 
Gene Names: JAK3
EC: 2.7.10.2
Find proteins for P52333 (Homo sapiens)
Explore P52333 
Go to UniProtKB:  P52333
NIH Common Fund Data Resources
PHAROS  P52333
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
G4Y
Query on G4Y

Download CCD File 
A
N-[(1S)-6-(5-phenyl-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-2,3-dihydro-1H-inden-1-yl]imidoformamide
C22 H19 N5
HLJVDQSXUUSDJP-IBGZPJMESA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.142α = 90
b = 75.137β = 90
c = 88.558γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
BUSTERrefinement
PDB_EXTRACTdata extraction
TRUNCATEdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2018-05-02 
  • Released Date: 2018-11-28 
  • Deposition Author(s): Vajdos, F.F.

Revision History 

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