4OYS

CRYSTAL STRUCTURE OF VPS34 IN COMPLEX WITH SAR405.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.180 

Starting Model: other
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

A highly potent and selective Vps34 inhibitor alters vesicle trafficking and autophagy.

Ronan, B.Flamand, O.Vescovi, L.Dureuil, C.Durand, L.Fassy, F.Bachelot, M.F.Lamberton, A.Mathieu, M.Bertrand, T.Marquette, J.P.El-Ahmad, Y.Filoche-Romme, B.Schio, L.Garcia-Echeverria, C.Goulaouic, H.Pasquier, B.

(2014) Nat Chem Biol 10: 1013-1019

  • DOI: https://doi.org/10.1038/nchembio.1681
  • Primary Citation of Related Structures:  
    4OYS

  • PubMed Abstract: 

    Vps34 is a phosphoinositide 3-kinase (PI3K) class III isoform that has attracted major attention over the recent years because of its role in autophagy. Herein we describe the biological characterization of SAR405, which is a low-molecular-mass kinase inhibitor of Vps34 (KD 1.5 nM). This compound has an exquisite protein and lipid kinase selectivity profile that is explained by its unique binding mode and molecular interactions within the ATP binding cleft of human Vps34. To the best of our knowledge, this is the first potent and specific Vps34 inhibitor described so far. Our results demonstrate that inhibition of Vps34 kinase activity by SAR405 affects both late endosome-lysosome compartments and prevents autophagy. Moreover, we show that the concomitant inhibition of Vps34 and mTOR, with SAR405 and the US Food and Drug Administration-approved mTOR inhibitor everolimus, results in synergistic antiproliferative activity in renal tumor cell lines, indicating a potential clinical application in cancer.


  • Organizational Affiliation

    Oncology Drug Discovery, Sanofi, Vitry Sur Seine, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphatidylinositol 3-kinase catalytic subunit type 3601Homo sapiensMutation(s): 0 
Gene Names: PIK3C3VPS34
EC: 2.7.1.137
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NEB9 (Homo sapiens)
Explore Q8NEB9 
Go to UniProtKB:  Q8NEB9
PHAROS:  Q8NEB9
GTEx:  ENSG00000078142 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8NEB9
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.180 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.81α = 90
b = 145.7β = 90
c = 61.78γ = 90
Software Package:
Software NamePurpose
PROCESSdata reduction
BUSTERrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-22
    Type: Initial release
  • Version 1.1: 2015-09-02
    Changes: Database references
  • Version 1.2: 2018-06-06
    Changes: Data collection, Derived calculations, Refinement description
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references
  • Version 1.4: 2024-03-27
    Changes: Refinement description