hALK in complex with compound 1 (S)-N-(1-(2,4-difluorophenyl)ethyl)-3-(3-methyl-1H-pyrazol-5-yl)imidazo[1,2-b]pyridazin-6-amine

Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.231 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.4 of the entry. See complete history


Discovery of Potent, Selective, and Brain-Penetrant 1 H-Pyrazol-5-yl-1 H-pyrrolo[2,3- b]pyridines as Anaplastic Lymphoma Kinase (ALK) Inhibitors.

Fushimi, M.Fujimori, I.Wakabayashi, T.Hasui, T.Kawakita, Y.Imamura, K.Kato, T.Murakami, M.Ishii, T.Kikko, Y.Kasahara, M.Nakatani, A.Hiura, Y.Miyamoto, M.Saikatendu, K.Zou, H.Lane, S.W.Lawson, J.D.Imoto, H.

(2019) J Med Chem 62: 4915-4935

  • DOI: https://doi.org/10.1021/acs.jmedchem.8b01630
  • Primary Citation of Related Structures:  
    6E0R, 6EBW, 6EDL

  • PubMed Abstract: 

    Anaplastic lymphoma kinase (ALK), a member of the receptor tyrosine kinase family, is predominantly expressed in the brain and implicated in neuronal development and cognition. However, the detailed function of ALK in the central nervous system (CNS) is still unclear. To elucidate the role of ALK in the CNS, it was necessary to discover a potent, selective, and brain-penetrant ALK inhibitor. Scaffold hopping and lead optimization of N-(2,4-difluorobenzyl)-3-(1 H-pyrazol-5-yl)imidazo[1,2- b]pyridazin-6-amine 1 guided by a cocrystal structure of compound 1 bound to ALK resulted in the identification of (6-(1-(5-fluoropyridin-2-yl)ethoxy)-1-(5-methyl-1 H-pyrazol-3-yl)-1 H-pyrrolo[2,3- b]pyridin-3-yl)((2 S)-2-methylmorpholin-4-yl)methanone 13 as a highly potent, selective, and brain-penetrable compound. Intraperitoneal administration of compound 13 significantly decreased the phosphorylated-ALK (p-ALK) levels in the hippocampus and prefrontal cortex in the mouse brain. These results suggest that compound 13 could serve as a useful chemical probe to elucidate the mechanism of ALK-mediated brain functions and the therapeutic potential of ALK inhibition.

  • Organizational Affiliation

    Neuroscience Drug Discovery Unit, Research , Takeda Pharmaceutical Company Limited , 26-1, Muraoka-Higashi 2-chome, Fujisawa , Kanagawa 251-8555 , Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ALK tyrosine kinase receptor322Homo sapiensMutation(s): 0 
Gene Names: ALK
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UM73 (Homo sapiens)
Explore Q9UM73 
Go to UniProtKB:  Q9UM73
GTEx:  ENSG00000171094 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UM73
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
J4M (Subject of Investigation/LOI)
Query on J4M

Download Ideal Coordinates CCD File 
B [auth A]N-[(1S)-1-(2,4-difluorophenyl)ethyl]-3-(5-methyl-1H-pyrazol-3-yl)imidazo[1,2-b]pyridazin-6-amine
C18 H16 F2 N6
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.231 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.571α = 90
b = 57.409β = 90
c = 103.41γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-01
    Type: Initial release
  • Version 1.1: 2019-05-08
    Changes: Data collection, Database references
  • Version 1.2: 2019-05-15
    Changes: Data collection, Database references
  • Version 1.3: 2019-06-05
    Changes: Data collection, Database references
  • Version 1.4: 2024-03-13
    Changes: Data collection, Database references