7QWK

GCN2 (EIF2ALPHA KINASE 4, E2AK4) IN COMPLEX WITH COMPOUND 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.214 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

The structure of human GCN2 reveals a parallel, back-to-back kinase dimer with a plastic DFG activation loop motif.

Maia de Oliveira, T.Korboukh, V.Caswell, S.Winter Holt, J.J.Lamb, M.Hird, A.W.Overman, R.

(2020) Biochem J 477: 275-284

  • DOI: https://doi.org/10.1042/BCJ20190196
  • Primary Citation of Related Structures:  
    7QQ6, 7QWK

  • PubMed Abstract: 

    When activated by amino acid starvation, the stress sensing protein kinase GCN2 phosphorylates the eukaryotic initiation factor 2 alpha, inhibiting translation to conserve energy and facilitate cell survival. Amino acid starvation, particularly of tryptophan and arginine, affects immune tolerance by suppressing differentiation and proliferation of T-cells via activation of GCN2 kinase. In addition, the GCN2 pathway mediates cancer survival directly within the context of metabolic stress. Here, we report the first crystal structures of the human GCN2 kinase domain (KD) in complex with two inhibitors of different size, shape, and chemical scaffold. Three novel activation loop conformations representative of different activation states of the kinase are described. In addition, a novel dimerization organization for GCN2 is observed. This arrangement is consistent with the hypothesis that the GCN2 KD forms an antiparallel inactive dimer until uncharged tRNA binds to it and triggers conformational changes that shift the equilibrium to the active parallel dimer.


  • Organizational Affiliation

    Structure, Biophysics and FBLG, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
eIF-2-alpha kinase GCN2
A, B, C, D, E
A, B, C, D, E, F, G, H
318Homo sapiensMutation(s): 1 
Gene Names: EIF2AK4GCN2KIAA1338
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9P2K8 (Homo sapiens)
Explore Q9P2K8 
Go to UniProtKB:  Q9P2K8
PHAROS:  Q9P2K8
GTEx:  ENSG00000128829 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9P2K8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
G41 (Subject of Investigation/LOI)
Query on G41

Download Ideal Coordinates CCD File 
I [auth A]
J [auth B]
K [auth C]
L [auth D]
M [auth E]
I [auth A],
J [auth B],
K [auth C],
L [auth D],
M [auth E],
N [auth F],
O [auth G],
P [auth H]
(2~{S})-~{N}-[(1~{S})-1-[4-[(6-pyridin-4-ylquinazolin-2-yl)amino]phenyl]ethyl]piperidine-2-carboxamide
C27 H28 N6 O
OQQHJQAFUOXHSI-BVZFJXPGSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
Q [auth H],
R [auth H]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.214 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.799α = 89.86
b = 77.795β = 90.05
c = 101.69γ = 68.58
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-04
    Type: Initial release
  • Version 2.0: 2023-07-12
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary
  • Version 2.1: 2024-02-07
    Changes: Data collection, Refinement description