4YMJ

(R)-2-Phenylpyrrolidine Substitute Imidazopyridazines: a New Class of Potent and Selective Pan-TRK Inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.165 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

(R)-2-Phenylpyrrolidine Substituted Imidazopyridazines: A New Class of Potent and Selective Pan-TRK Inhibitors.

Choi, H.S.Rucker, P.V.Wang, Z.Fan, Y.Albaugh, P.Chopiuk, G.Gessier, F.Sun, F.Adrian, F.Liu, G.Hood, T.Li, N.Jia, Y.Che, J.McCormack, S.Li, A.Li, J.Steffy, A.Culazzo, A.Tompkins, C.Phung, V.Kreusch, A.Lu, M.Hu, B.Chaudhary, A.Prashad, M.Tuntland, T.Liu, B.Harris, J.Seidel, H.M.Loren, J.Molteni, V.

(2015) Acs Med.Chem.Lett. 6: 562-567

  • DOI: 10.1021/acsmedchemlett.5b00050
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Deregulated kinase activities of tropomyosin receptor kinase (TRK) family members have been shown to be associated with tumorigenesis and poor prognosis in a variety of cancer types. In particular, several chromosomal rearrangements involving TRKA ha ...

    Deregulated kinase activities of tropomyosin receptor kinase (TRK) family members have been shown to be associated with tumorigenesis and poor prognosis in a variety of cancer types. In particular, several chromosomal rearrangements involving TRKA have been reported in colorectal, papillary thyroid, glioblastoma, melanoma, and lung tissue that are believed to be the key oncogenic driver in these tumors. By screening the Novartis compound collection, a novel imidazopyridazine TRK inhibitor was identified that served as a launching point for drug optimization. Structure guided drug design led to the identification of (R)-2-phenylpyrrolidine substituted imidazopyridazines as a series of potent, selective, orally bioavailable pan-TRK inhibitors achieving tumor regression in rats bearing KM12 xenografts. From this work the (R)-2-phenylpyrrolidine has emerged as an ideal moiety to incorporate in bicyclic TRK inhibitors by virtue of its shape complementarity to the hydrophobic pocket of TRKs.


    Organizational Affiliation

    Genomics Institute of the Novartis Research Foundation , 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
304Homo 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 3 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
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
4EJ
Query on 4EJ

Download SDF File 
Download CCD File 
A, B
4-[6-(benzylamino)imidazo[1,2-b]pyridazin-3-yl]benzonitrile
C20 H15 N5
OXQTXNVWTNDAQF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
A, B
L-PEPTIDE LINKINGC3 H8 N O6 PSER
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
4EJIC50: 100 nM (95) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.165 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 65.610α = 90.00
b = 65.610β = 90.00
c = 175.622γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
HKL-2000data reduction
MOLREPphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-06-03
    Type: Initial release