6N3O

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

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: 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 inhibi ...

    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.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
eIF-2-alpha kinase GCN2 A317Homo sapiensMutation(s): 4 
Gene Names: EIF2AK4, GCN2, KIAA1338
EC: 2.7.11.1
Find proteins for Q9P2K8 (Homo sapiens)
Explore Q9P2K8 
Go to UniProtKB:  Q9P2K8
NIH Common Fund Data Resources
PHAROS:  Q9P2K8
GTEx:  ENSG00000128829
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KA7
Query on KA7
Download Ideal Coordinates CCD File 
A
N-{3-[(2-aminopyrimidin-5-yl)ethynyl]-2,4-difluorophenyl}-5-chloro-2-methoxypyridine-3-sulfonamide
C18 H12 Cl F2 N5 O3 S
JGHVXJKGYJYWOP-UHFFFAOYSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
KA7IC50:  2.4000000953674316   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.899α = 90
b = 82.899β = 90
c = 193.702γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

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