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 
  • R-Value Observed: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.1 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.

(2019) J Med Chem 62: 247-265

  • DOI: 10.1021/acs.jmedchem.8b00280
  • Structures With Same Primary Citation

  • 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

    Pfizer Global R&D, Groton Laboratories , Eastern Point Road , Groton , Connecticut 06340 , United States.



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: NTRK1MTCTRKTRKA
EC: 2.7.10.1
Find proteins for P04629 (Homo sapiens)
Go to UniProtKB:  P04629
NIH Common Fund Data Resources
PHAROS  P04629
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FQG
Query on FQG

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 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 
  • R-Value Observed: 0.172 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.94α = 90
b = 45.81β = 127.04
c = 79.49γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling
BUSTERrefinement
PDB_EXTRACTdata extraction
BUSTERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-05-02
    Type: Initial release
  • Version 1.1: 2019-05-01
    Changes: Data collection, Database references