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(-) Description

Title :  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
 
Authors :  B. Pasquier, Y. El-Ahmad, B. Filoche-Romme, C. Dureuil, F. Fassy, P. Y. Abecassis, M. Mathieu, T. Bertrand, T. Benard, C. Barriere, S. El J. P. Letallec, V. Sonnefraud, M. Brollo, L. Delbarre, V. Loyau, F. Pil L. Bertin, P. Richepin, J. Arigon, J. R. Labrosse, J. Clement, F. Duran R. Combet, P. Perraut, V. Leroy, F. Gay, D. Lefrancois, F. Bretin, J. P. Marquette, N. Michot, A. Caron, C. Castell, L. Schio, G. Mccort, H. Goulaouic, C. Garcia-Echeverria, B. Ronan
Date :  12 Aug 14  (Deposition) - 26 Nov 14  (Release) - 21 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.93
Chains :  Asym./Biol. Unit :  A
Keywords :  Transferase, Lipid Kinase, Autophagy Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Pasquier, Y. El-Ahmad, B. Filoche-Romme, C. Dureuil-Sizaire, F. Fassy, P. Abecassis, M. Mathieu, T. Bertrand, T. Benard, C. Barriere, S. El Batti, J. Letallec, V. Sonnefraud, M. Brollo, L. Delbarre, V. Loyau, F. Pilorge, L. Bertin, P. Richepin, J. Arigon, J. Labrosse, J. Clement, F. Durand, R. Combet, P. Perraut, V. Leroy, F. Gay, D. Lefrancois, F. Bretin, J. Marquette, N. Michot, A. Caron, C. Castell, L. Schio, G. Mccort, H. Goulaouic, C. Garcia-Echeverria, B. P. Ronan
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.
J. Med. Chem. V. 58 376 2015
PubMed-ID: 25402320  |  Reference-DOI: 10.1021/JM5013352

(-) Compounds

Molecule 1 - PHOSPHATIDYLINOSITOL 3-KINASE CATALYTIC SUBUNIT TYPE 3
    Chains: A
    EC Number: 2.7.1.137
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: VPS34 HELICAL AND KINASE DOMAINS, RESIDUES 282-879
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PI3-KINASE TYPE 3, PI3K TYPE 3, PTDINS-3-KINASE TYPE 3, PHO SPHATIDYLINOSITOL 3-KINASE P100 SUBUNIT, PHOSPHOINOSITIDE-3-KINASE CLASS 3, HVPS34, PHOSPHOINOSITIDE 3-KINASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1JXM1Ligand/Ion(8S)-9-[(2R)-2-HYDROXY-2-PHENYLETHYL]-2-(MORPHOLIN-4-YL)-8-(TRIFLUOROMETHYL)-6,7,8,9-TETRAHYDRO-4H-PYRIMIDO[1,2-A]PYRIMIDIN-4-ONE
2NA2Ligand/IonSODIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:659 , LEU A:667 , HOH A:2271 , HOH A:2272 , HOH A:2273 , HOH A:2280BINDING SITE FOR RESIDUE NA A1874
2AC2SOFTWAREGLU A:439 , HIS A:857 , SER A:861 , HOH A:2117 , HOH A:2119 , HOH A:2128BINDING SITE FOR RESIDUE NA A1875
3AC3SOFTWAREPHE A:612 , PRO A:618 , ILE A:634 , LYS A:636 , TYR A:670 , MET A:682 , GLN A:683 , PHE A:684 , ILE A:685 , SER A:687 , LEU A:750 , ILE A:760 , ASP A:761 , HOH A:2248 , HOH A:2260 , HOH A:2320BINDING SITE FOR RESIDUE JXM A1876

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4UWH)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4UWH)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4UWH)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4UWH)

(-) Exons   (0, 0)

(no "Exon" information available for 4UWH)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:554
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh.....hhhhhhhh......hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh......eee..eeeeeeeee.hhhhee.......eeeeeee....eeeeeeee...hhhhhhhhhhhhhhhhhhhhh..........eee....eeeee....eehhhhhhhhhhhhhhhhhhh....hhhh.hhhhhhhhhhhhhhhhhhhhhh.........eee.....eee....................hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4uwh A 285 DLKPNAATRDQLNIIVSYPPTKQLTYEEQDLVWKFRYYLTNQEKALTKFLKCVNWDLPQEAKQALELLGKWKPMDVEDSLELLSSHYTNPTVRRYAVARLRQADDEDLLMYLLQLVQALKYENFDDIKNGLEPINSAEIDSSQIITSPLPNLEQDLCTFLISRACKNSTLANYLYWYVIVECEDQDTQQRDPKTHEMYLNVMRRFSQALLKGDKSVRVMRSLLAAQQTFVDRLVHLMKAVQRESGNRKKKNERLQALLGDNEKMNLSDVELIPLPLEPQVKIRGIIPETATLFKSALMPAQLFFKTEDGGKYPVIFKHGDDLRQDQLILQIISLMDKLLRKENLDLKLTPYKVLATSTKHGFMQFIQSVPVAEVLDTEGSIQNFFRKYAPSENGPNGISAEVMDTYVKSCAGYCVITYILGVGDRHLDNLLLTKTGKLFHIDFGYILGRDPKPLPPPMKLNKEMVEGMGGTQSEQYQEFRKQCYTAFLHLRRYSNLILNLFSLMVDANIPDIALEPDKTVKKVQDKFRLDLSDEEAVHYMQSLIDESVHALFAA 873
                                   294       304       314       324       334       344       354       364       374       384       394       404       414  ||   441       451|      479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719       729       739       749       759       769       779       789       799       809       819       829       839       849       859       869    
                                                                                                                                                              417|             451|                                                                                                                                                                                                                                                                                                                                                                                                                   
                                                                                                                                                               435              470
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4UWH)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4UWH)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4UWH)

(-) Gene Ontology  (40, 40)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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UniProtKB/Swiss-Prot
        PK3C3_HUMAN | Q8NEB9: 3ihy 3ls8 4oys 4ph4 4uwf 4uwg 4uwk 4uwl 5anl 5enn

(-) Related Entries Specified in the PDB File

4uwk 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
4uwl 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