4YMJ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1021/acsmedchemlett.5b00050
  • Primary Citation of Related Structures:  
    4YMJ, 4YNE, 4YPS

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NT-3 growth factor receptor
A, B
304Homo sapiensMutation(s): 0 
Gene Names: NTRK3TRKC
EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q16288 (Homo sapiens)
Explore Q16288 
Go to UniProtKB:  Q16288
PHAROS:  Q16288
GTEx:  ENSG00000140538 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16288
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
4EJ
Query on 4EJ

Download Ideal Coordinates CCD File 
C [auth A],
H [auth B]
4-[6-(benzylamino)imidazo[1,2-b]pyridazin-3-yl]benzonitrile
C20 H15 N5
OXQTXNVWTNDAQF-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
I [auth B]
J [auth B]
D [auth A],
E [auth A],
F [auth A],
I [auth B],
J [auth B],
K [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
G [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
A, B
L-PEPTIDE LINKINGC3 H8 N O6 PSER
Binding Affinity Annotations 
IDSourceBinding Affinity
4EJ BindingDB:  4YMJ IC50: 100 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.61α = 90
b = 65.61β = 90
c = 175.622γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-06-03
    Type: Initial release
  • Version 1.1: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy
  • Version 1.2: 2024-11-20
    Changes: Structure summary