5ADZ | pdb_00005adz

Ether Lipid-Generating Enzyme AGPS in complex with inhibitor 1a

• PDB DOI: https://doi.org/10.2210/pdb5ADZ/pdb

• Classification: TRANSFERASE
• Organism(s): Cavia porcellus
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2015-08-25 Released: 2015-09-23 
• Deposition Author(s): Piano, V., Benjamin, D.I., Valente, S., Nenci, S., Marrocco, B., Mai, A., Aliverti, A., Nomura, D.K., Mattevi, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.253 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

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

• PubMed: 26322624 
• DOI: https://doi.org/10.1021/acschembio.5b00466
• Primary Citation Related Structures: 
  5ADZ, 5AE1, 5AE2, 5AE3


• 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 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.

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Organizational Affiliation: 
• Department of Biology and Biotechnology, University of Pavia , via Ferrata 9, 27100 Pavia, Italy.
Program in Metabolic Biology, Department of Nutritional Sciences and Toxicology, University of California, Berkeley , Berkeley, California 94720, United States.
Department of Drug Chemistry and Technologies, University "La Sapienza" , P. le A. Moro 5, Roma 00185, Italy.
Pasteur Institute, Cenci Bolognetti Foundation , P.le A. Moro 5, Roma 00185, Italy.
Department of Biosciences, University of Milano , Via Festa del Perdono, 7, 20122 Milano, Italy.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 296.21 kDa 
• Atom Count: 18,475 
• Modeled Residue Count: 2,217 
• Deposited Residue Count: 2,632 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE, PEROXISOMAL	A, B, C, D	658	Cavia porcellus	Mutation(s): 0  EC: 2.5.1.26
UniProt
Find proteins for P97275 (Cavia porcellus) Explore P97275  Go to UniProtKB:  P97275

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	E [auth A], G [auth B], I [auth C], K [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
KQS	F [auth A], H [auth B], J [auth C], L [auth D]	(3S)-3-(2-fluorophenyl)-N-((2-oxo-2,3-dihydro-1H-benzo[d]imidazol-5-yl)methyl)butanamide) C18 H18 F N3 O2 JYQMTEASQYBLAO-NSHDSACASA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.253 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.06	α = 90.57
b = 99.61	β = 90.04
c = 107.97	γ = 94.76

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-09-23 
Deposition Author(s): Piano, V., Benjamin, D.I., Valente, S., Nenci, S., Marrocco, B., Mai, A., Aliverti, A., Nomura, D.K., Mattevi, A.

Revision History  

• Version 1.0: 2015-09-23
  Type: Initial release
  
• Version 1.1: 2015-12-02
  Changes: Database references
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description