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 (IC <sub>50 </sub>=0.7nM), with ∼175-fold improvement in Pyk2 potency as com ...

    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 (IC 50 =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., 199 East Blaine Street, Seattle, WA 98102, USA.,Department of Biology, Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA.,Department of Structural Chemistry, Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA.,Department of Drug Metabolism, Gilead Sciences, Inc., 199 East Blaine Street, Seattle, WA 98102, USA.,Department of Medicinal Chemistry, Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA.,Department of Biology, Gilead Sciences, Inc., 199 East Blaine Street, Seattle, WA 98102, USA.,Department of Medicinal Chemistry, Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA. Electronic address: Julie.Farand@gilead.com.,Department of Structural Chemistry, Gilead Sciences, Inc., 199 East Blaine Street, Seattle, WA 98102, USA.




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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
YAMIC50: 13 nM BINDINGMOAD
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