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 

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:  

  • 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: 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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0YJ
Query on 0YJ

Download SDF File 
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: 530 nM (96) BINDINGDB
0YJIC50: 78 nM BINDINGMOAD
0YJIC50: 78 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.223 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 37.393α = 90.00
b = 81.429β = 90.00
c = 86.396γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHASERphasing
HKL-2000data collection
BUSTERrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Database references