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 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


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

  • 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). Moreove ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tyrosine-protein kinase receptorAB308Homo sapiensMutation(s): 0 
Gene Names: NTRK1MTCTRKTRKA
EC: 2.7.10.1
Find proteins for P04629 (Homo sapiens)
Explore P04629 
Go to UniProtKB:  P04629
NIH Common Fund Data Resources
PHAROS  P04629
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 CCD File 
A, 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
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

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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