5JFX

Crystal structure of TrkA in complex with PF-06273340


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

The Discovery of a Potent, Selective, and Peripherally Restricted Pan-Trk Inhibitor (PF-06273340) for the Treatment of Pain.

Skerratt, S.E.Andrews, M.Bagal, S.K.Bilsland, J.Brown, D.Bungay, P.J.Cole, S.Gibson, K.R.Jones, R.Morao, I.Nedderman, A.Omoto, K.Robinson, C.Ryckmans, T.Skinner, K.Stupple, P.Waldron, G.

(2016) J. Med. Chem. 59: 10084-10099

  • DOI: 10.1021/acs.jmedchem.6b00850
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The neurotrophin family of growth factors, comprised of nerve growth factor (NGF), brain derived neurotrophic factor (BDNF), neurotrophin 3 (NT3), and neurotrophin 4 (NT4), is implicated in the physiology of chronic pain. Given the clinical efficacy ...

    The neurotrophin family of growth factors, comprised of nerve growth factor (NGF), brain derived neurotrophic factor (BDNF), neurotrophin 3 (NT3), and neurotrophin 4 (NT4), is implicated in the physiology of chronic pain. Given the clinical efficacy of anti-NGF monoclonal antibody (mAb) therapies, there is significant interest in the development of small molecule modulators of neurotrophin activity. Neurotrophins signal through the tropomyosin related kinase (Trk) family of tyrosine kinase receptors, hence Trk kinase inhibition represents a potentially "druggable" point of intervention. To deliver the safety profile required for chronic, nonlife threatening pain indications, highly kinase-selective Trk inhibitors with minimal brain availability are sought. Herein we describe how the use of SBDD, 2D QSAR models, and matched molecular pair data in compound design enabled the delivery of the highly potent, kinase-selective, and peripherally restricted clinical candidate PF-06273340.


    Organizational Affiliation

    Pfizer Global Research & Development , The Portway Building, Granta Park, Great Abington, Cambridge, CB21 6GS, U.K.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
High affinity nerve growth factor receptor
A
308Homo sapiensMutation(s): 0 
Gene Names: NTRK1 (MTC, TRK, TRKA)
EC: 2.7.10.1
Find proteins for P04629 (Homo sapiens)
Go to Gene View: NTRK1
Go to UniProtKB:  P04629
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6K4
Query on 6K4

Download SDF File 
Download CCD File 
A
N-{5-[2-amino-7-(1-hydroxy-2-methylpropan-2-yl)-7H-pyrrolo[2,3-d]pyrimidine-5-carbonyl]pyridin-3-yl}-2-(5-chloropyridin-2-yl)acetamide
C23 H22 Cl N7 O3
BPIWZDNVMQQBQX-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
6K4IC50: 6 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.201 
  • Space Group: P 64
Unit Cell:
Length (Å)Angle (°)
a = 125.013α = 90.00
b = 125.013β = 90.00
c = 46.216γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
SCALAdata scaling
BUSTERrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-03-01
    Type: Initial release