6DKI

Crystal structure of Trk-A in complex with the Pan-Trk Kinase Inhibitor, compound 19.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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). 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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
High affinity nerve growth factor receptorA320Homo sapiensMutation(s): 0 
Gene Names: NTRK1MTCTRKTRKA
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOD (Subject of Investigation/LOI)
Query on GOD

Download Ideal Coordinates CCD File 
C [auth A]6-amino-5-{[(3S)-4,4-difluoro-1-{[4-(trifluoromethoxy)phenyl]acetyl}pyrrolidin-3-yl]oxy}-N-methylpyridine-3-carboxamide
C20 H19 F5 N4 O4
FTAFQADCGCSJAH-HNNXBMFYSA-N
 Ligand Interaction
22L (Subject of Investigation/LOI)
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
OLGMRBGIXZANNV-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
GOD BindingDB:  6DKI Kd: min: 2.3, max: 5.7 (nM) from 2 assay(s)
IC50: 8.4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.64α = 90
b = 45.51β = 126.56
c = 79.32γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
SCALAdata scaling
Cootmodel building
BUSTERphasing

Structure Validation

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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