5TOB

Selectivity switch between FAK and Pyk2: Macrocyclization of FAK inhibitors improves Pyk2 potency


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.117 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Selectivity switch between FAK and Pyk2: Macrocyclization of FAK inhibitors improves Pyk2 potency.

Farand, J.Mai, N.Chandrasekhar, J.Newby, Z.E.Van Veldhuizen, J.Loyer-Drew, J.Venkataramani, C.Guerrero, J.Kwok, A.Li, N.Zherebina, Y.Wilbert, S.Zablocki, J.Phillips, G.Watkins, W.J.Mourey, R.Notte, G.T.

(2016) Bioorg. Med. Chem. Lett. 26: 5926-5930

  • DOI: 10.1016/j.bmcl.2016.10.092
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Herein, we describe the synthesis of Pyk2 inhibitors via macrocyclization of FAK and dual Pyk2-FAK inhibitors. We identified macrocycle 25a as a highly potent Pyk2 inhibitor (IC50=0.7nM), with ∼175-fold improvement in Pyk2 potency as compared to its ...

    Herein, we describe the synthesis of Pyk2 inhibitors via macrocyclization of FAK and dual Pyk2-FAK inhibitors. We identified macrocycle 25a as a highly potent Pyk2 inhibitor (IC50=0.7nM), with ∼175-fold improvement in Pyk2 potency as compared to its acyclic counterpart. In many cases, macrocyclization improved Pyk2 potency while weakening FAK potency, thereby improving the Pyk2/FAK selectivity ratio for this structural class of inhibitors. Various macrocyclic linkers were studied in an attempt to optimize Pyk2 selectivity. We observed macrocyclic atropisomerism during the synthesis of 19-membered macrocycles 10a-d, and successfully obtained crystallographic evidence of one atropisomer (10a-AtropB) preferentially bound to Pyk2.


    Organizational Affiliation

    Department of Medicinal Chemistry, Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA. Electronic address: Julie.Farand@gilead.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein-tyrosine kinase 2-beta
A
282Homo 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
YAM
Query on YAM

Download SDF File 
Download CCD File 
A
N-methyl-N-{3-[({2-[(2-oxo-2,3-dihydro-1H-indol-5-yl)amino]-5-(trifluoromethyl)pyrimidin-4-yl}amino)methyl]pyridin-2-yl}methanesulfonamide
C21 H20 F3 N7 O3 S
MZDKLVOWGIOKTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.117 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.206 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 37.584α = 90.00
b = 93.808β = 92.53
c = 42.519γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
EPMRphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2016-10-17 
  • Released Date: 2017-11-29 
  • Deposition Author(s): Newby, Z.E.

Revision History 

  • Version 1.0: 2017-11-29
    Type: Initial release