3ET7 | pdb_00003et7

Crystal structure of PYK2 complexed with PF-2318841


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.328 (Depositor), 0.320 (DCC) 
  • R-Value Work: 
    0.247 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 
    0.251 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 349Click on this verticalbar to view details

This is version 1.2 of the entry. See complete history


Literature

Trifluoromethylpyrimidine-based inhibitors of proline-rich tyrosine kinase 2 (PYK2): structure-activity relationships and strategies for the elimination of reactive metabolite formation.

Walker, D.P.Bi, F.C.Kalgutkar, A.S.Bauman, J.N.Zhao, S.X.Soglia, J.R.Aspnes, G.E.Kung, D.W.Klug-McLeod, J.Zawistoski, M.P.McGlynn, M.A.Oliver, R.Dunn, M.Li, J.C.Richter, D.T.Cooper, B.A.Kath, J.C.Hulford, C.A.Autry, C.L.Luzzio, M.J.Ung, E.J.Roberts, W.G.Bonnette, P.C.Buckbinder, L.Mistry, A.Griffor, M.C.Han, S.Guzman-Perez, A.

(2008) Bioorg Med Chem Lett 18: 6071-6077

  • DOI: https://doi.org/10.1016/j.bmcl.2008.10.030
  • Primary Citation of Related Structures:  
    3ET7

  • PubMed Abstract: 

    The synthesis and SAR for a series of diaminopyrimidines as PYK2 inhibitors are described. Using a combination of library and traditional medicinal chemistry techniques, a FAK-selective chemical series was transformed into compounds possessing good PYK2 potency and 10- to 20-fold selectivity against FAK. Subsequent studies found that the majority of the compounds were positive in a reactive metabolite assay, an indicator for potential toxicological liabilities. Based on the proposed mechanism for bioactivation, as well as a combination of structure-based drug design and traditional medicinal chemistry techniques, a follow-up series of PYK2 inhibitors was identified that maintained PYK2 potency, FAK selectivity and HLM stability, yet were negative in the RM assay.


  • Organizational Affiliation

    Pfizer Global Research and Development, Eastern Point Road, Groton, CT 06340, USA. daniel.p.walker@pfizer.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein tyrosine kinase 2 beta277Homo sapiensMutation(s): 0 
Gene Names: PTK2BFAK2PYK2RAFTK
EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q14289 (Homo sapiens)
Explore Q14289 
Go to UniProtKB:  Q14289
PHAROS:  Q14289
GTEx:  ENSG00000120899 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14289
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
349
Query on 349

Download Ideal Coordinates CCD File 
B [auth A]5-{[4-{[2-(pyrrolidin-1-ylsulfonyl)benzyl]amino}-5-(trifluoromethyl)pyrimidin-2-yl]amino}-1,3-dihydro-2H-indol-2-one
C24 H21 F3 N6 O3 S
TWFBJYGVNVQOCW-UHFFFAOYSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
C [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.328 (Depositor), 0.320 (DCC) 
  • R-Value Work:  0.247 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 0.251 (Depositor) 
Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.824α = 90
b = 106.824β = 90
c = 75.185γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 349Click on this verticalbar to view details

Entry History 

Deposition Data

  • Released Date: 2009-06-23 
  • Deposition Author(s): Han, S.

Revision History  (Full details and data files)

  • Version 1.0: 2009-06-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-12-27
    Changes: Data collection, Database references, Derived calculations