Crystal structure of TrkA in complex with PF-05206283

Experimental Data Snapshot

  • Resolution: 1.59 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 

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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: 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.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
High affinity nerve growth factor receptor308Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P04629 (Homo sapiens)
Explore P04629 
Go to UniProtKB:  P04629
PHAROS:  P04629
GTEx:  ENSG00000198400 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04629
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 6K1

Download Ideal Coordinates CCD File 
B [auth A]N-{5-[4-amino-7-(propan-2-yl)-7H-pyrrolo[2,3-d]pyrimidine-5-carbonyl]pyridin-3-yl}-2-(4-chlorophenyl)acetamide
C23 H21 Cl N6 O2
Binding Affinity Annotations 
IDSourceBinding Affinity
6K1 Binding MOAD:  5JFV IC50: 6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.59 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 
  • Space Group: P 64
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.54α = 90
b = 124.54β = 90
c = 46.42γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-01
    Type: Initial release
  • Version 1.1: 2024-03-06
    Changes: Data collection, Database references