3FZS

Crystal Structure of PYK2 complexed with BIRB796

  • Classification: TRANSFERASE
  • Organism(s): Homo sapiens
  • Mutation(s): No 

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 

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:  
    3FZO, 3FZP, 3FZR, 3FZS, 3FZT

  • 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:  (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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
B96
Query on B96

Download CCD File 
A
1-(5-TERT-BUTYL-2-P-TOLYL-2H-PYRAZOL-3-YL)-3-[4-(2-MORPHOLIN-4-YL-ETHOXY)-NAPHTHALEN-1-YL]-UREA
C31 H37 N5 O3
MVCOAUNKQVWQHZ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
B96Kd:  990   nM  BindingDB
B96IC50 :  1500   nM  PDBBind
B96IC50:  1500   nM  Binding MOAD
B96IC50:  11500   nM  BindingDB
B96IC50:  400   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.503α = 90
b = 81.694β = 90
c = 87.256γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report



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
    Changes: Version format compliance