4UWF

Discovery of (2S)-8-((3R)-3-Methylmorpholin-4-yl)-1-(3-methyl-2-oxo- butyl)-2-(trifluoromethyl)-3,4-dihydro-2H-pyrimido(1,2-a)pyrimidin-6- one: a Novel Potent and Selective Inhibitor of Vps34 for the Treatment of Solid Tumors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.215 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Discovery of (2S)-8-[(3R)-3-Methylmorpholin-4-Yl]-1-(3-Methyl-2-Oxobutyl)-2-(Trifluoromethyl)-3,4-Dihydro-2H-Pyrimido[1,2-A]Pyrimidin-6-One: A Novel Potent and Selective Inhibitor of Vps34 for the Treatment of Solid Tumors.

Pasquier, B.El-Ahmad, Y.Filoche-Romme, B.Dureuil, C.Fassy, F.Abecassis, P.Mathieu, M.Bertrand, T.Benard, T.Barriere, C.El Batti, S.Letallec, J.Sonnefraud, V.Brollo, M.Delbarre, L.Loyau, V.Pilorge, F.Bertin, L.Richepin, P.Arigon, J.Labrosse, J.Clement, J.Durand, F.Combet, R.Perraut, P.Leroy, V.Gay, F.Lefrancois, D.Bretin, F.Marquette, J.Michot, N.Caron, A.Castell, C.Schio, L.Mccort, G.Goulaouic, H.Garcia-Echeverria, C.Ronan, B.

(2015) J Med Chem 58: 376

  • DOI: 10.1021/jm5013352
  • Primary Citation of Related Structures:  
    4UWF, 4UWG, 4UWH, 4UWK, 4UWL

  • PubMed Abstract: 
  • Vps34 (the human class III phosphoinositide 3-kinase) is a lipid kinase involved in vesicle trafficking and autophagy and therefore constitutes an interesting target for cancer treatment. Because of the lack of specific Vps34 kinase inhibitors, we aimed to identify such compounds to further validate the role of this lipid kinase in cancer maintenance and progression ...

    Vps34 (the human class III phosphoinositide 3-kinase) is a lipid kinase involved in vesicle trafficking and autophagy and therefore constitutes an interesting target for cancer treatment. Because of the lack of specific Vps34 kinase inhibitors, we aimed to identify such compounds to further validate the role of this lipid kinase in cancer maintenance and progression. Herein, we report the discovery of a series of tetrahydropyrimidopyrimidinone derivatives. Starting with hit compound 1a, medicinal chemistry optimization led to compound 31. This molecule displays potent activity, an exquisite selectivity for Vps34 with excellent properties. The X-ray crystal structure of compound 31 in human Vps34 illustrates how the unique molecular features of the morpholine synthon bestows selectivity against class I PI3Ks. This molecule exhibits suitable in vivo mouse PK parameters and induces a sustained inhibition of Vps34 upon acute administration. Compound 31 constitutes an optimized Vps34 inhibitor that could be used to investigate human cancer biology.


    Organizational Affiliation

    Oncology Drug Discovery, ‡Drug Disposition and Safety, §Structure Design Informatics and Structural Biology, ∥Pharmaceutical Sciences Operations, ⊥Protein Production, and #Global Biotherapeutic, Sanofi , 13 Quai Jules Guesde, 94403 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
Find proteins for Q8NEB9 (Homo sapiens)
Explore Q8NEB9 
Go to UniProtKB:  Q8NEB9
NIH Common Fund Data Resources
PHAROS  Q8NEB9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EUT
Query on EUT

Download CCD File 
A
(8S)-9-[3,5-bis(fluoranyl)phenyl]-2-morpholin-4-yl-8-(trifluoromethyl)-7,8-dihydro-6H-pyrimido[1,2-a]pyrimidin-4-one
C18 H17 F5 N4 O2
XTBZCKNQFVGNFT-AWEZNQCLSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.215 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.735α = 90
b = 145.87β = 90
c = 61.343γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History 

  • Version 1.0: 2014-11-26
    Type: Initial release
  • Version 1.1: 2015-01-21
    Changes: Database references
  • Version 1.2: 2019-05-08
    Changes: Data collection, Experimental preparation, Other