Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 32.72 kDa 
• Atom Count: 2359 
• Residue Count: 254 
• Unique protein chains: 1

3FZS

Crystal Structure of PYK2 complexed with BIRB796

• DOI: 10.2210/pdb3FZS/pdb

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


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

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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 

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

• PubMed: 19244237 
• 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-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.

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Organizational Affiliation: 

Pfizer Global Research & Development, Groton, CT 06340, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein tyrosine kinase 2 beta	A	277	Homo sapiens	Mutation(s): 0  Gene Names: PTK2B, FAK2, PYK2, RAFTK EC: 2.7.10.2
Find proteins for Q14289 (Homo sapiens) Explore Q14289  Go to UniProtKB:  Q14289
NIH Common Fund Data Resources
PHAROS  Q14289 GTEx  ENSG00000120899

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
B96	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

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
B96	Kd:  990   nM  BindingDB
B96	IC50 :  1500   nM  PDBBind
B96	IC50:  1500   nM  Binding MOAD
B96	IC50:  11500   nM  BindingDB
B96	IC50:  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 = 37.503	α = 90
b = 81.694	β = 90
c = 87.256	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

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