Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 35.58 kDa 
• Atom Count: 2,571 
• Modelled Residue Count: 277 
• Deposited Residue Count: 308 
• Unique protein chains: 1

 5JFX

Crystal structure of TrkA in complex with PF-06273340

• PDB DOI:  https://doi.org/10.2210/pdb5JFX/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2016-04-19 Released: 2017-03-01 
• Deposition Author(s): Jayasankar, J., Kurumbail, R., Skerratt, S., Brown, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free: 0.232 
• R-Value Work: 0.201 
• R-Value Observed: 0.203 

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

• PubMed: 27766865 
• DOI: https://doi.org/10.1021/acs.jmedchem.6b00850
• Primary Citation of Related Structures:  
  5JFS, 5JFV, 5JFW, 5JFX


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
High affinity nerve growth factor receptor	A	308	Homo sapiens	Mutation(s): 0  Gene Names: NTRK1, MTC, TRK, TRKA EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P04629 (Homo sapiens) Explore P04629  Go to UniProtKB:  P04629
PHAROS:  P04629

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6K4	B [auth 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

Binding Affinity Annotations
ID	Source	Binding Affinity
6K4	Binding MOAD:  5JFX	IC50: 6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free: 0.232 
• R-Value Work: 0.201 
• R-Value Observed: 0.203 
• Space Group: P 6₄

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.013	α = 90
b = 125.013	β = 90
c = 46.216	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-03-01 
Deposition Author(s): Jayasankar, J., Kurumbail, R., Skerratt, S., Brown, D.

Revision History  

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