6GOU | pdb_00006gou

Development of Alkyl Glycerone Phosphate Synthase Inhibitors: Complex with Inhibitor 2I


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 
    0.258 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.219 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.221 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted FADClick on this verticalbar to view detailsBest fitted F6TClick on this verticalbar to view details

This is version 1.1 of the entry. See complete history


Literature

Development of alkyl glycerone phosphate synthase inhibitors: Structure-activity relationship and effects on ether lipids and epithelial-mesenchymal transition in cancer cells.

Stazi, G.Battistelli, C.Piano, V.Mazzone, R.Marrocco, B.Marchese, S.Louie, S.M.Zwergel, C.Antonini, L.Patsilinakos, A.Ragno, R.Viviano, M.Sbardella, G.Ciogli, A.Fabrizi, G.Cirilli, R.Strippoli, R.Marchetti, A.Tripodi, M.Nomura, D.K.Mattevi, A.Mai, A.Valente, S.

(2018) Eur J Med Chem 163: 722-735

  • DOI: https://doi.org/10.1016/j.ejmech.2018.11.050
  • Primary Citation of Related Structures:  
    6GOU

  • PubMed Abstract: 

    In aggressive tumors, alkylglyceronephosphate synthase (AGPS) controls cellular ether phospholipid utilization and metabolism to promote cancer cell proliferation and motility. SAR studies on the first-in-class AGPS inhibitor 1, discovered by our group, led to the 2,6-difluoro analog 2i which showed higher binding affinity than 1in vitro. In 231MFP cancer cells, 2i reduced ether lipids levels and cell migration rate. When tested in PC-3 and MDA-MB-231 cancer cells, 2i specifically impaired epithelial to mesenchymal transition (EMT) by modulating E-cadherin, Snail and MMP2 expression levels. Moreover, the combination of siRNAs against AGPS and 2i provided no additive effect, confirming that the modulation of 2i on EMT specifically relies on AGPS inhibition. Finally, this compound also affected cancer cell proliferation especially in MDA-MB-231 cells expressing higher AGPS level, whereas it provided negligible effects on MeT5A, a non-tumorigenic cell line, thus showing cancer specificity.


  • Organizational Affiliation

    Department of Chemistry and Technologies of Drugs, Sapienza University of Rome, P. le A. Moro 5, 00185, Rome, Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alkyldihydroxyacetonephosphate synthase, peroxisomalA [auth D],
B [auth A],
C [auth B],
D [auth C]
658Cavia porcellusMutation(s): 0 
Gene Names: AGPS
EC: 2.5.1.26
UniProt
Find proteins for P97275 (Cavia porcellus)
Explore P97275 
Go to UniProtKB:  P97275
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP97275
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
E [auth D],
G [auth A],
I [auth B],
K [auth C]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
F6T
Query on F6T

Download Ideal Coordinates CCD File 
F [auth D],
H [auth A],
J [auth B]
(3~{S})-3-[2,6-bis(fluoranyl)phenyl]-~{N}-[(2-oxidanylidene-1,3-dihydrobenzimidazol-5-yl)methyl]butanamide
C18 H17 F2 N3 O2
VDLFVZUKOKPJRH-JTQLQIEISA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free:  0.258 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.219 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.221 (Depositor) 
Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 147.958α = 90
b = 120.644β = 95.27
c = 148.16γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
Aimlessdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted FADClick on this verticalbar to view detailsBest fitted F6TClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Italian Association for Cancer ResearchItalyFellowship 18022

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-02
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Data collection, Database references, Refinement description