5H5S

Crystal structure of human GPX4 in complex with GXpep-3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery of GPX4 inhibitory peptides from random peptide T7 phage display and subsequent structural analysis

Sakamoto, K.Sogabe, S.Kamada, Y.Matsumoto, S.I.Kadotani, A.Sakamoto, J.I.Tani, A.

(2017) Biochem. Biophys. Res. Commun. 482: 195-201

  • DOI: 10.1016/j.bbrc.2016.11.035
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The phospholipid hydroperoxidase glutathione peroxidase (GPX4) is an enzyme that reduces lipid hydroperoxides in lipid membranes. Recently, GPX4 has been investigated as a target molecule that induces iron-dependent cell death (ferroptosis) selective ...

    The phospholipid hydroperoxidase glutathione peroxidase (GPX4) is an enzyme that reduces lipid hydroperoxides in lipid membranes. Recently, GPX4 has been investigated as a target molecule that induces iron-dependent cell death (ferroptosis) selectively in cancer cells that express mutant Ras. GPX4 inhibitors have the potential to become novel anti-cancer drugs. However, there are no druggable pockets for conventional small molecules on the molecular surface of GPX4. To generate GPX4 inhibitors, we examined the use of peptides as an alternative to small molecules. By screening peptide libraries displayed on T7 phages, and analyzing the X-ray crystal structures of the peptides, we successfully identified one peptide that binds to near Sec73 of catalytic site and two peptides that bind to another site on GPX4. To our knowledge, this is the first study reporting GPX4 inhibitory peptides and their structural information.


    Organizational Affiliation

    Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, 251-8555, Japan. Electronic address: koutarou.sakamoto@takeda.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phospholipid hydroperoxide glutathione peroxidase, mitochondrial
A
169Homo sapiensMutation(s): 8 
Gene Names: GPX4
EC: 1.11.1.12
Find proteins for P36969 (Homo sapiens)
Go to Gene View: GPX4
Go to UniProtKB:  P36969
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
GXpep-3
B
14N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSD
Query on CSD
A
L-PEPTIDE LINKINGC3 H7 N O4 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.166 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 35.017α = 90.00
b = 39.077β = 97.84
c = 59.394γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
SCALEPACKdata scaling
REFMACrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-12-07
    Type: Initial release
  • Version 1.1: 2017-01-11
    Type: Database references