Crystal structure of Trk-A in complex with the Pan-Trk Kinase Inhibitor, compound 13b.

Experimental Data Snapshot

  • Resolution: 2.53 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.1 of the entry. See complete history


Discovery of Potent, Selective, and Peripherally Restricted Pan-Trk Kinase Inhibitors for the Treatment of Pain.

Bagal, S.K.Andrews, M.Bechle, B.M.Bian, J.Bilsland, J.Blakemore, D.C.Braganza, J.F.Bungay, P.J.Corbett, M.S.Cronin, C.N.Cui, J.J.Dias, R.Flanagan, N.J.Greasley, S.E.Grimley, R.James, K.Johnson, E.Kitching, L.Kraus, M.L.McAlpine, I.Nagata, A.Ninkovic, S.Omoto, K.Scales, S.Skerratt, S.E.Sun, J.Tran-Dube, M.Waldron, G.J.Wang, F.Warmus, J.S.

(2018) J Med Chem 61: 6779-6800

  • DOI: https://doi.org/10.1021/acs.jmedchem.8b00633
  • Primary Citation of Related Structures:  
    6DKB, 6DKG, 6DKI, 6DKW

  • PubMed Abstract: 

    Hormones of the neurotrophin family, nerve growth factor (NGF), brain derived neurotrophic factor (BDNF), neurotrophin 3 (NT3), and neurotrophin 4 (NT4), are known to activate the family of Tropomyosin receptor kinases (TrkA, TrkB, and TrkC). Moreover, inhibition of the TrkA kinase pathway in pain has been clinically validated by the NGF antibody tanezumab, leading to significant interest in the development of small molecule inhibitors of TrkA. Furthermore, Trk inhibitors having an acceptable safety profile will require minimal brain availability. Herein, we discuss the discovery of two potent, selective, peripherally restricted, efficacious, and well-tolerated series of pan-Trk inhibitors which successfully delivered three candidate quality compounds 10b, 13b, and 19. All three compounds are predicted to possess low metabolic clearance in human that does not proceed via aldehyde oxidase-catalyzed reactions, thus addressing the potential clearance prediction liability associated with our current pan-Trk development candidate PF-06273340.

  • Organizational Affiliation

    Pfizer Worldwide R&D U.K. , The Portway Building, Granta Park , 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 receptor320Homo 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 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GO7 (Subject of Investigation/LOI)
Query on GO7

Download Ideal Coordinates CCD File 
C [auth A]2-{[(3R,4S)-3-fluoro-1-{[4-(trifluoromethoxy)phenyl]acetyl}piperidin-4-yl]oxy}-4-(2-hydroxy-2-methylpropoxy)benzamide
C25 H28 F4 N2 O6
Query on 22L

Download Ideal Coordinates CCD File 
B [auth A]5-phenylthieno[2,3-d]pyrimidin-4(3H)-one
C12 H8 N2 O S
Binding Affinity Annotations 
IDSourceBinding Affinity
GO7 BindingDB:  6DKG Kd: min: 1.1, max: 2.6 (nM) from 2 assay(s)
IC50: 7700 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.53 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.189 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.28α = 90
b = 45.49β = 125.97
c = 78.54γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
Cootmodel building

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-11
    Type: Initial release
  • Version 1.1: 2018-08-15
    Changes: Data collection, Database references