2X6J

THE CRYSTAL STRUCTURE OF THE DROSOPHILA CLASS III PI3-KINASE VPS34 IN COMPLEX WITH PIK-93


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.230 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Shaping Development of Autophagy Inhibitors with the Structure of the Lipid Kinase Vps34.

Miller, S.Tavshanjian, B.Oleksy, A.Perisic, O.Houseman, B.T.Shokat, K.M.Williams, R.L.

(2010) Science 327: 1638

  • DOI: 10.1126/science.1184429
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Phosphoinositide 3-kinases (PI3Ks) are lipid kinases with diverse roles in health and disease. The primordial PI3K, Vps34, is present in all eukaryotes and has essential roles in autophagy, membrane trafficking, and cell signaling. We solved the crys ...

    Phosphoinositide 3-kinases (PI3Ks) are lipid kinases with diverse roles in health and disease. The primordial PI3K, Vps34, is present in all eukaryotes and has essential roles in autophagy, membrane trafficking, and cell signaling. We solved the crystal structure of Vps34 at 2.9 angstrom resolution, which revealed a constricted adenine-binding pocket, suggesting the reason that specific inhibitors of this class of PI3K have proven elusive. Both the phosphoinositide-binding loop and the carboxyl-terminal helix of Vps34 mediate catalysis on membranes and suppress futile adenosine triphosphatase cycles. Vps34 appears to alternate between a closed cytosolic form and an open form on the membrane. Structures of Vps34 complexes with a series of inhibitors reveal the reason that an autophagy inhibitor preferentially inhibits Vps34 and underpin the development of new potent and specific Vps34 inhibitors.


    Organizational Affiliation

    Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHOSPHOTIDYLINOSITOL 3 KINASE 59F
A, B
696Drosophila melanogasterMutation(s): 1 
Gene Names: Pi3K59F (Dmel\CG5373, DmVps34, dPI3K, dVps34, PI(3)K, PI3K, PI3K-59F, PI3K59F, Pi3k59F, PI3K_59F, Pi3K_59F, PI[[3]]K, PIK359F, VPS34, Vps34, vps34)
EC: 2.7.1.137
Find proteins for Q9W1M7 (Drosophila melanogaster)
Go to UniProtKB:  Q9W1M7
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
093
Query on 093

Download SDF File 
Download CCD File 
A, B
N-(5-(4-CHLORO-3-(2-HYDROXY-ETHYLSULFAMOYL)- PHENYLTHIAZOLE-2-YL)-ACETAMIDE
PIK-93; N-[(2Z)-5-(4-CHLORO-3-{[(2-HYDROXYETHYL)AMINO]SULFONYL}PHENYL)-4-METHYL-1,3-THIAZOL-2(3H)-YLIDENE]ACETAMIDE
C14 H16 Cl N3 O4 S2
JFVNFXCESCXMBC-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
93IC50: 36 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.230 
  • Space Group: I 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 109.950α = 90.00
b = 156.330β = 90.00
c = 242.910γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
SCALAdata scaling
REFMACrefinement
iMOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-04-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2018-01-24
    Type: Source and taxonomy