Identification of novel, potent and selective GCN2 inhibitors as first-in-class anti-tumor agents

Experimental Data Snapshot

  • Resolution: 2.61 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.226 

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Ligand Structure Quality Assessment 

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Identification of Novel, Potent, and Orally Available GCN2 Inhibitors with Type I Half Binding Mode.

Fujimoto, J.Kurasawa, O.Takagi, T.Liu, X.Banno, H.Kojima, T.Asano, Y.Nakamura, A.Nambu, T.Hata, A.Ishii, T.Sameshima, T.Debori, Y.Miyamoto, M.Klein, M.G.Tjhen, R.Sang, B.C.Levin, I.Lane, S.W.Snell, G.P.Li, K.Kefala, G.Hoffman, I.D.Ding, S.C.Cary, D.R.Mizojiri, R.

(2019) ACS Med Chem Lett 10: 1498-1503

  • DOI: https://doi.org/10.1021/acsmedchemlett.9b00400
  • Primary Citation of Related Structures:  
    6N3L, 6N3N, 6N3O

  • PubMed Abstract: 

    General control nonderepressible 2 (GCN2) is a master regulator kinase of amino acid homeostasis and important for cancer survival in the tumor microenvironment under amino acid depletion. We initiated studies aiming at the discovery of novel GCN2 inhibitors as first-in-class antitumor agents and conducted modification of the substructure of sulfonamide derivatives with expected type I half binding on GCN2. Our synthetic strategy mainly corresponding to the αC-helix allosteric pocket of GCN2 led to significant enhancement in potency and a good pharmacokinetic profile in mice. In addition, compound 6d , which showed slow dissociation in binding on GCN2, demonstrated antiproliferative activity in combination with the asparagine-depleting agent asparaginase in an acute lymphoblastic leukemia (ALL) cell line, and it also displayed suppression of GCN2 pathway activation with asparaginase treatment in the ALL cell line and mouse xenograft model.

  • Organizational Affiliation

    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
eIF-2-alpha kinase GCN2,eIF-2-alpha kinase GCN2
A, B
330Homo sapiensMutation(s): 4 
Gene Names: EIF2AK4GCN2KIAA1338
UniProt & NIH Common Fund Data Resources
Find proteins for Q9P2K8 (Homo sapiens)
Explore Q9P2K8 
Go to UniProtKB:  Q9P2K8
GTEx:  ENSG00000128829 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9P2K8
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KAV (Subject of Investigation/LOI)
Query on KAV

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C23 H19 F3 N6 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 2.61 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.226 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.886α = 90
b = 122.233β = 90
c = 120.674γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-09
    Type: Initial release
  • Version 1.1: 2019-10-30
    Changes: Data collection, Database references