3ET7

Crystal structure of PYK2 complexed with PF-2318841


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.328 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.251 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Trifluoromethylpyrimidine-based inhibitors of proline-rich tyrosine kinase 2 (PYK2): structure-activity relationships and strategies for the elimination of reactive metabolite formation.

Walker, D.P.Bi, F.C.Kalgutkar, A.S.Bauman, J.N.Zhao, S.X.Soglia, J.R.Aspnes, G.E.Kung, D.W.Klug-McLeod, J.Zawistoski, M.P.McGlynn, M.A.Oliver, R.Dunn, M.Li, J.C.Richter, D.T.Cooper, B.A.Kath, J.C.Hulford, C.A.Autry, C.L.Luzzio, M.J.Ung, E.J.Roberts, W.G.Bonnette, P.C.Buckbinder, L.Mistry, A.Griffor, M.C.Han, S.Guzman-Perez, A.

(2008) Bioorg Med Chem Lett 18: 6071-6077

  • DOI: 10.1016/j.bmcl.2008.10.030
  • Primary Citation of Related Structures:  
    3ET7

  • PubMed Abstract: 
  • The synthesis and SAR for a series of diaminopyrimidines as PYK2 inhibitors are described. Using a combination of library and traditional medicinal chemistry techniques, a FAK-selective chemical series was transformed into compounds possessing good P ...

    The synthesis and SAR for a series of diaminopyrimidines as PYK2 inhibitors are described. Using a combination of library and traditional medicinal chemistry techniques, a FAK-selective chemical series was transformed into compounds possessing good PYK2 potency and 10- to 20-fold selectivity against FAK. Subsequent studies found that the majority of the compounds were positive in a reactive metabolite assay, an indicator for potential toxicological liabilities. Based on the proposed mechanism for bioactivation, as well as a combination of structure-based drug design and traditional medicinal chemistry techniques, a follow-up series of PYK2 inhibitors was identified that maintained PYK2 potency, FAK selectivity and HLM stability, yet were negative in the RM assay.


    Organizational Affiliation

    Pfizer Global Research and Development, Eastern Point Road, Groton, CT 06340, USA. daniel.p.walker@pfizer.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein tyrosine kinase 2 betaA277Homo sapiensMutation(s): 0 
Gene Names: PTK2BFAK2PYK2RAFTK
EC: 2.7.10.2
Find proteins for Q14289 (Homo sapiens)
Explore Q14289 
Go to UniProtKB:  Q14289
NIH Common Fund Data Resources
PHAROS  Q14289
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
349
Query on 349

Download CCD File 
A
5-{[4-{[2-(pyrrolidin-1-ylsulfonyl)benzyl]amino}-5-(trifluoromethyl)pyrimidin-2-yl]amino}-1,3-dihydro-2H-indol-2-one
C24 H21 F3 N6 O3 S
TWFBJYGVNVQOCW-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
349IC50 :  17   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.328 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.251 
  • Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.824α = 90
b = 106.824β = 90
c = 75.185γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2008-10-07 
  • Released Date: 2009-06-23 
  • Deposition Author(s): Han, S.

Revision History 

  • Version 1.0: 2009-06-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance