4H1M

Crystal structure of PYK2 with the indole 10c


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.226 

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
  • Primary Citation of Related Structures:  
    4H1M, 4H1J

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein-tyrosine kinase 2-betaA293Homo 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
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0YJ
Query on 0YJ

Download CCD File 
A
7-({[3-tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-yl]carbamoyl}amino)-N-(propan-2-yl)-1H-indole-2-carboxamide
C27 H32 N6 O2
WGABQSVUYBMTBW-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0YJIC50 :  78   nM  PDBBind
0YJIC50:  530   nM  BindingDB
0YJIC50:  78   nM  BindingDB
0YJIC50:  78   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.226 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.393α = 90
b = 81.429β = 90
c = 86.396γ = 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