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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 :  2.80
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 Plasmid: PET
    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, PHOSPHATIDYLINOSITOL 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
17A51Ligand/Ion(8S)-2-[(3R)-3-METHYLMORPHOLIN-4-YL]-9-(3-METHYL-2-OXOBUTYL)-8-(TRIFLUOROMETHYL)-6,7,8,9-TETRAHYDRO-4H-PYRIMIDO[1,2-A]PYRIMIDIN-4-ONE
2SO42Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:393 , TYR A:496 , GLN A:649 , LYS A:671 , HOH A:2036 , HOH A:2040BINDING SITE FOR RESIDUE SO4 A1870
2AC2SOFTWARELYS A:613 , SER A:614 , 7A5 A:1872BINDING SITE FOR RESIDUE SO4 A1871
3AC3SOFTWAREPHE A:612 , SER A:614 , PRO A:618 , ILE A:634 , TYR A:670 , MET A:682 , GLN A:683 , ILE A:685 , LEU A:750 , ILE A:760 , ASP A:761 , SO4 A:1871 , HOH A:2033BINDING SITE FOR RESIDUE 7A5 A1872

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4UWL)

(-) 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:543
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhh......hhhhhhhhhhh..hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh...hhhhhhhhhh....hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh......eee..eeeeeeeee.....ee.......eeeeeee....eeeeeeee...hhhhhhhhhhhhhhhhhhhhh..........eee....eeeee....eehhhhhhhhhhhhhhhhhhh....hhhh.hhhhhhhhhhhhhhhhhhhhhh.........eee.....eee....................hhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhh...hhhhhhhhhh....hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4uwl A 286 LKPNAATRDQLNIIVSYPPTKQLTYEEQDLVWKFRYYLTNQEKALTKFLKCVNWDLPQEAKQALELLGKWKPMDVEDSLELLSSHYTNPTVRRYAVARLRQADDEDLLMYLLQLVQALKYENFDDIKNGLEEIDSSQIITSPLPLEQDLCTFLISRACKNSTLANYLYWYVIVECEDQDTQQRDPKTHEMYLNVMRRFSQALLKGDKSVRVMRSLLAAQQTFVDRLVHLMKAVQRESGNRKKKNERLQALLGDNEKMNLSDVELIPLPLEPQVKIRGIIPETATLFKSALMPAQLFFKTEDGGKYPVIFKHGDDLRQDQLILQIISLMDKLLRKENLDLKLTPYKVLATSTKHGFMQFIQSVPVAEVLDTEGSIQNFFRKYAPSENGPNGISAEVMDTYVKSCAGYCVITYILGVGDRHLDNLLLTKTGKLFHIDFGYILGRDPKPLPPPMKLNKEMVEGMGGTQSEQYQEFRKQCYTAFLHLRRYSNLILNLFSLMVDANIPDIALEPDKTVKKVQDKFRLDLSDEEAVHYMQSLIDESVHA 869
                                   295       305       315       325       335       345       355       365       375       385       395       405       415||     447   ||  476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776       786       796       806       816       826       836       846       856       866   
                                                                                                                                                            416|         451|                                                                                                                                                                                                                                                                                                                                                                                                              
                                                                                                                                                             439          471
   Legend:   → Mismatch (orange background)
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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 4UWL)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 4uwh 4uwk 5anl 5enn

(-) Related Entries Specified in the PDB File

4uwh 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
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