4YPS

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

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:  
    4YNE, 4YMJ, 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 ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
High affinity nerve growth factor receptorA303Homo sapiensMutation(s): 0 
Gene Names: NTRK1MTCTRKTRKA
EC: 2.7.10.1
Find proteins for P04629 (Homo sapiens)
Explore P04629 
Go to UniProtKB:  P04629
NIH Common Fund Data Resources
PHAROS:  P04629
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4F6
Query on 4F6

Download Ideal Coordinates CCD File 
B [auth A]4-{6-[(3R)-3-(3-fluorophenyl)morpholin-4-yl]imidazo[1,2-b]pyridazin-3-yl}benzonitrile
C23 H18 F N5 O
OGLFUDJJJDTBFS-NRFANRHFSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A], D [auth A], E [auth A], F [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
4F6IC50:  75   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.481α = 90
b = 106.481β = 90
c = 204.511γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

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