3V5Q

Discovery of a selective TRK Inhibitor with efficacy in rodent cancer tumor models


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2001 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery of GNF-5837, a Selective TRK Inhibitor with Efficacy in Rodent Cancer Tumor Models.

Albaugh, P.Fan, Y.Mi, Y.Sun, F.Adrian, F.Li, N.Jia, Y.Sarkisova, Y.Kreusch, A.Hood, T.Lu, M.Liu, G.Huang, S.Liu, Z.Loren, J.Tuntland, T.Karanewsky, D.S.Seidel, H.M.Molteni, V.

(2012) ACS Med Chem Lett 3: 140-145

  • DOI: 10.1021/ml200261d

  • PubMed Abstract: 
  • Neurotrophins and their receptors (TRKs) play key roles in the development of the nervous system and the maintenance of the neural network. Accumulating evidence points to their role in malignant transformations, chemotaxis, metastasis, and survival ...

    Neurotrophins and their receptors (TRKs) play key roles in the development of the nervous system and the maintenance of the neural network. Accumulating evidence points to their role in malignant transformations, chemotaxis, metastasis, and survival signaling and may contribute to the pathogenesis of a variety of tumors of both neural and non-neural origin. By screening the GNF kinase collection, a series of novel oxindole inhibitors of TRKs were identified. Optimization led to the identification of GNF-5837 (22), a potent, selective, and orally bioavailable pan-TRK inhibitor that inhibited tumor growth in a mouse xenograft model derived from RIE cells expressing both TRKA and NGF. The properties of 22 make it a good tool for the elucidation of TRK biology in cancer and other nononcology indications.


    Organizational Affiliation

    Genomics Institute of the Novartis Research Foundation (GNF), 10675 John Jay Hopkins Drive, San Diego, California 92121, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NT-3 growth factor receptor
A, B
297Homo sapiensMutation(s): 0 
Gene Names: NTRK3 (TRKC)
EC: 2.7.10.1
Find proteins for Q16288 (Homo sapiens)
Go to Gene View: NTRK3
Go to UniProtKB:  Q16288
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
0F4
Query on 0F4

Download SDF File 
Download CCD File 
A, B
1-(3-{[(3Z)-2-oxo-3-(1H-pyrrol-2-ylmethylidene)-2,3-dihydro-1H-indol-6-yl]amino}phenyl)-3-[3-(trifluoromethyl)phenyl]urea
C27 H20 F3 N5 O2
JCRUDKWPDBIGME-UCQKPKSFSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0F4IC50: 40 nM (95) BINDINGDB
0F4IC50: 40 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2001 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.212 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 65.580α = 90.00
b = 65.580β = 90.00
c = 177.252γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
PHENIXrefinement
MOLREPphasing
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2011-12-16 
  • Released Date: 2012-02-08 
  • Deposition Author(s): Kreusch, A.

Revision History 

  • Version 1.0: 2012-02-08
    Type: Initial release
  • Version 1.1: 2018-01-24
    Type: Database references