4H1J

Crystal structure of PYK2 with the pyrazole 13a


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Identification of novel series of pyrazole and indole-urea based DFG-out PYK2 inhibitors.

Bhattacharya, S.K.Aspnes, G.E.Bagley, S.W.Boehm, M.Brosius, A.D.Buckbinder, L.Chang, J.S.Dibrino, J.Eng, H.Frederick, K.S.Griffith, D.A.Griffor, M.C.Guimaraes, C.R.Guzman-Perez, A.Han, S.Kalgutkar, A.S.Klug-McLeod, J.Garcia-Irizarry, C.Li, J.Lippa, B.Price, D.A.Southers, J.A.Walker, D.P.Wei, L.Xiao, J.Zawistoski, M.P.Zhao, X.

(2012) Bioorg Med Chem Lett 22: 7523-7529

  • DOI: 10.1016/j.bmcl.2012.10.039
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Previous drug discovery efforts identified classical PYK2 kinase inhibitors such as 2 and 3 that possess selectivity for PYK2 over its intra-family isoform FAK. Efforts to identify more kinome-selective chemical matter that stabilize a DFG-out confor ...

    Previous drug discovery efforts identified classical PYK2 kinase inhibitors such as 2 and 3 that possess selectivity for PYK2 over its intra-family isoform FAK. Efforts to identify more kinome-selective chemical matter that stabilize a DFG-out conformation of the enzyme are described herein. Two sub-series of PYK2 inhibitors, an indole carboxamide-urea and a pyrazole-urea have been identified and found to have different binding interactions with the hinge region of PYK2. These leads proved to be more selective than the original classical inhibitors.


    Organizational Affiliation

    Worldwide Medicinal Chemistry, Pfizer Global Research and Development, 620 Memorial Drive, Cambridge, MA 02139, United States. samit.k.bhattacharya@pfizer.com



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein-tyrosine kinase 2-beta
A
293Homo sapiensMutation(s): 0 
Gene Names: PTK2BFAK2PYK2RAFTK
EC: 2.7.10.2
Find proteins for Q14289 (Homo sapiens)
Go to UniProtKB:  Q14289
NIH Common Fund Data Resources
PHAROS  Q14289
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0YH
Query on 0YH

Download CCD File 
A
1-[3-tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-yl]-3-[3-(4-methoxy-2-methylphenyl)-1H-pyrazol-5-yl]urea
C26 H30 N6 O2
LATBWIWKSPOPNK-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0YHIC50 :  1200   nM  PDBBind
0YHIC50:  1200   nM  Binding MOAD
0YHIC50:  1200   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.945α = 90
b = 82.923β = 90
c = 85.728γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
BUSTERrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2012-09-10 
  • Released Date: 2012-11-28 
  • Deposition Author(s): Han, S.

Revision History 

  • Version 1.0: 2012-11-28
    Type: Initial release
  • Version 1.1: 2012-12-12
    Changes: Database references