3FZR

Crystal structure of PYK2 complexed with PF-431396

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Structural characterization of proline-rich tyrosine kinase 2 (PYK2) reveals a unique (DFG-out) conformation and enables inhibitor design.

Han, S., Mistry, A., Chang, J.S., Cunningham, D., Griffor, M., Bonnette, P.C., Wang, H., Chrunyk, B.A., Aspnes, G.E., Walker, D.P., Brosius, A.D., Buckbinder, L.

(2009) J.Biol.Chem. 284: 13193-13201

  • DOI: 10.1074/jbc.M809038200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Proline-rich tyrosine kinase 2 (PYK2) is a cytoplasmic, non-receptor tyrosine kinase implicated in multiple signaling pathways. It is a negative regulator of osteogenesis and considered a viable drug target for osteoporosis treatment. The high-resolu ...

    Proline-rich tyrosine kinase 2 (PYK2) is a cytoplasmic, non-receptor tyrosine kinase implicated in multiple signaling pathways. It is a negative regulator of osteogenesis and considered a viable drug target for osteoporosis treatment. The high-resolution structures of the human PYK2 kinase domain with different inhibitor complexes establish the conventional bilobal kinase architecture and show the conformational variability of the DFG loop. The basis for the lack of selectivity for the classical kinase inhibitor, PF-431396, within the FAK family is explained by our structural analyses. Importantly, the novel DFG-out conformation with two diarylurea inhibitors (BIRB796, PF-4618433) reveals a distinct subclass of non-receptor tyrosine kinases identifiable by the gatekeeper Met-502 and the unique hinge loop conformation of Leu-504. This is the first example of a leucine residue in the hinge loop that blocks the ATP binding site in the DFG-out conformation. Our structural, biophysical, and pharmacological studies suggest that the unique features of the DFG motif, including Leu-504 hinge-loop variability, can be exploited for the development of selective protein kinase inhibitors.

    Organizational Affiliation: 

    Pfizer Global Research & Development, Groton, CT 06340, USA. seungil.han@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
3JZ
Query on 3JZ
Download SDF File 
Download CCD File 
A
N-methyl-N-{2-[({2-[(2-oxo-2,3-dihydro-1H-indol-5-yl)amino]-5-(trifluoromethyl)pyrimidin-4-yl}amino)methyl]phenyl}methanesulfonamide
C22 H21 F3 N6 O3 S
POJZIZBONPAWIV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3JZIC50: 11 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.211 
  • Space Group: P 4 21 2
Unit Cell:
Length (Å)Angle (°)
a = 107.326α = 90.00
b = 107.326β = 90.00
c = 75.786γ = 90.00
Software Package:
Software NamePurpose
BUSTER-TNTrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2009-01-26 
  • Released Date: 2009-03-31 
  • Deposition Author(s): Han, S.

Revision History 

  • Version 1.0: 2009-03-31
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance