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 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 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: 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 ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phosphatidylinositol 3-kinase catalytic subunit type 3A601Homo 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1TT (Subject of Investigation/LOI)
Query on 1TT

Download Ideal Coordinates CCD File 
F [auth A](8S)-9-[(5-chloranylpyridin-3-yl)methyl]-2-[(3R)-3-methylmorpholin-4-yl]-8-(trifluoromethyl)-6,7,8,9a-tetrahydro-3H-pyrimido[1,2-a]pyrimidin-4-one
C19 H23 Cl F3 N5 O2
HTJGYDUKBSAZGM-MRAWALMUSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A], C [auth A], D [auth A], E [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
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

View Full Validation Report



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