5AE1

Ether Lipid-Generating Enzyme AGPS in complex with inhibitor ZINC69435460


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery of Inhibitors for the Ether Lipid-Generating Enzyme Agps as Anti-Cancer Agents.

Piano, V.Benjamin, D.I.Valente, S.Nenci, S.Marrocco, B.Mai, A.Aliverti, A.Nomura, D.K.Mattevi, A.

(2015) Acs Chem.Biol. 10: 2589

  • DOI: 10.1021/acschembio.5b00466
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Dysregulated ether lipid metabolism is an important hallmark of cancer cells. Previous studies have reported that lowering ether lipid levels by genetic ablation of the ether lipid-generating enzyme alkyl-glycerone phosphate synthase (AGPS) lowers ke ...

    Dysregulated ether lipid metabolism is an important hallmark of cancer cells. Previous studies have reported that lowering ether lipid levels by genetic ablation of the ether lipid-generating enzyme alkyl-glycerone phosphate synthase (AGPS) lowers key structural and oncogenic ether lipid levels and alters fatty acid, glycerophospholipid, and eicosanoid metabolism to impair cancer pathogenicity, indicating that AGPS may be a potential therapeutic target for cancer. In this study, we have performed a small-molecule screen to identify candidate AGPS inhibitors. We have identified several lead AGPS inhibitors and have structurally characterized their interactions with the enzyme and show that these inhibitors bind to distinct portions of the active site. We further show that the lead AGPS inhibitor 1a selectively lowers ether lipid levels in several types of human cancer cells and impairs their cellular survival and migration. We provide here the first report of in situ-active pharmacological tools for inhibiting AGPS, which may provide chemical scaffolds for future AGPS inhibitor development for cancer therapy.


    Organizational Affiliation

    Department of Biology and Biotechnology, University of Pavia , via Ferrata 9, 27100 Pavia, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE, PEROXISOMAL
A, B, C, D
658Cavia porcellusMutation(s): 0 
Gene Names: AGPS
EC: 2.5.1.26
Find proteins for P97275 (Cavia porcellus)
Go to Gene View: AGPS
Go to UniProtKB:  P97275
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
B2Z
Query on B2Z

Download SDF File 
Download CCD File 
A, B, C, D
(3-(2-FLUOROPHENYL)-N-(1-(2-OXO-2,3-DIHYDRO-1H-BENZO[D]IMIDAZOL-5-YL)ETHYL)BUTANAMIDE)
C19 H20 F N3 O2
QMZGJDIRPYTWRL-NWDGAFQWSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
FAD
Query on FAD

Download SDF File 
Download CCD File 
A, B, C, D
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.186 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 60.790α = 90.64
b = 99.020β = 89.96
c = 107.020γ = 95.49
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PHASERphasing
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-09-09
    Type: Initial release
  • Version 1.1: 2015-12-02
    Type: Database references