3ET7

Crystal structure of PYK2 complexed with PF-2318841


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.328 
  • R-Value Work: 0.247 

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

  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein tyrosine kinase 2 beta
A
277Homo sapiensMutation(s): 0 
Gene Names: PTK2B (FAK2, PYK2, RAFTK)
EC: 2.7.10.2
Find proteins for Q14289 (Homo sapiens)
Go to Gene View: PTK2B
Go to UniProtKB:  Q14289
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
349
Query on 349

Download SDF File 
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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
349IC50: 17 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.328 
  • R-Value Work: 0.247 
  • Space Group: P 4 21 2
Unit Cell:
Length (Å)Angle (°)
a = 106.824α = 90.00
b = 106.824β = 90.00
c = 75.185γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
REFMACrefinement
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Version format compliance