6DKW

Crystal structure of Trk-A in complex with the Pan-Trk Kinase Inhibitor, compound 3.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.233 

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Literature

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 ...

    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, Groton Laboratories , Eastern Point Road , Groton , Connecticut 06340 , United States.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tyrosine-protein kinase receptorA, B308Homo sapiensMutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04629
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GXA
Query on GXA
Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]		5-(1-methyl-1H-imidazol-4-yl)-2-[(1-{[4-(trifluoromethoxy)phenyl]acetyl}piperidin-4-yl)oxy]benzamide
C25 H25 F3 N4 O4
VXJAFFGXYYHGQN-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
GXA BindingDB:  6DKW IC50: 7 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.233 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.98α = 90
b = 93.98β = 90
c = 159.27γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
SCALAdata scaling
Cootmodel building
BUSTERphasing

Structure Validation

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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