6D20

Crystal structure of Tyrosine-protein kinase receptor in complex with 5-(4-fluorophenyl)thieno[2,3-d]pyrimidin-4(3H)-one and 5-{[2,4-dichloro-5-(pyridin-2-yl)benzene-1-carbonyl]amino}-N-(2-hydroxy-2-methylpropyl)-1-phenyl-1H-pyrazole-3-carboxamide Inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Discovery of Allosteric, Potent, Subtype Selective and Peripherally Restricted TrkA Kinase Inhibitors.

Bagal, S.K.Omoto, K.Blakemore, D.C.Bungay, P.J.Bilsland, J.G.Clarke, P.J.Corbett, M.S.Cronin, C.N.Cui, J.J.Dias, R.Flanagan, N.J.Greasley, S.E.Grimley, R.Johnson, E.Fengas, D.Kitching, L.Kraus, M.L.McAlpine, I.Nagata, A.Waldron, G.J.Warmus, J.S.

(2018) J. Med. Chem. --: --

  • DOI: 10.1021/acs.jmedchem.8b00280
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Tropomyosin receptor kinases (TrkA, TrkB, TrkC) are activated by hormones of the neurotrophin family: nerve growth factor (NGF), brain derived neurotrophic factor (BDNF), neurotrophin 3 (NT3), and neurotrophin 4 (NT4). Moreover, the NGF antibody tane ...

    Tropomyosin receptor kinases (TrkA, TrkB, TrkC) are activated by hormones of the neurotrophin family: nerve growth factor (NGF), brain derived neurotrophic factor (BDNF), neurotrophin 3 (NT3), and neurotrophin 4 (NT4). Moreover, the NGF antibody tanezumab has provided clinical proof of concept for inhibition of the TrkA kinase pathway in pain leading to significant interest in the development of small molecule inhibitors of TrkA. However, achieving TrkA subtype selectivity over TrkB and TrkC via a Type I and Type II inhibitor binding mode has proven challenging and Type III or Type IV allosteric inhibitors may present a more promising selectivity design approach. Furthermore, TrkA inhibitors with minimal brain availability are required to deliver an appropriate safety profile. Herein, we describe the discovery of a highly potent, subtype selective, peripherally restricted, efficacious, and well-tolerated series of allosteric TrkA inhibitors that culminated in the delivery of candidate quality compound 23.


    Organizational Affiliation

    Worldwide Medicinal Chemistry , Pfizer Global R&D U.K. , The Portway Building, Granta Park , Cambridge CB21 6GS , U.K.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
High affinity nerve growth factor receptor
A
320Homo sapiensMutation(s): 0 
Gene Names: NTRK1 (MTC, TRK, TRKA)
EC: 2.7.10.1
Find proteins for P04629 (Homo sapiens)
Go to Gene View: NTRK1
Go to UniProtKB:  P04629
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FQG
Query on FQG

Download SDF File 
Download CCD File 
A
5-{[2,4-dichloro-5-(pyridin-2-yl)benzene-1-carbonyl]amino}-N-(2-hydroxy-2-methylpropyl)-1-phenyl-1H-pyrazole-3-carboxamide
C26 H23 Cl2 N5 O3
NXDRKVFQQJUBOG-UHFFFAOYSA-N
 Ligand Interaction
FQD
Query on FQD

Download SDF File 
Download CCD File 
A
5-(4-fluorophenyl)thieno[2,3-d]pyrimidin-4(3H)-one
C12 H7 F N2 O S
DARIIFLATJJEOB-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.170 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 113.940α = 90.00
b = 45.810β = 127.04
c = 79.490γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
BUSTERphasing
PDB_EXTRACTdata extraction
BUSTERrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-05-02
    Type: Initial release