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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 :  2.99
Chains :  Asym./Biol. Unit :  A
Keywords :  Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Pasquier, Y. El-Ahmad, B. Filoche-Romme, C. Dureuil, 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. Ronan
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.
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, 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  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1EUT1Ligand/Ion(8S)-9-[3,5-BIS(FLUORANYL)PHENYL]-2-MORPHOLIN-4-YL-8-(TRIFLUOROMETHYL)-7,8-DIHYDRO-6H-PYRIMIDO[1,2-A]PYRIMIDIN-4-ONE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:612 , SER A:614 , PRO A:618 , ILE A:634 , LYS A:636 , TYR A:670 , MET A:682 , GLN A:683 , PHE A:684 , ILE A:685 , PRO A:689 , ASP A:747 , LEU A:750 , ILE A:760 , ASP A:761 , HOH A:2054BINDING SITE FOR RESIDUE EUT A4000

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4UWF)

(-) 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:550
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh.......hhhhhhhhhhh..hhhhhhhhhhhhh......hhhhhhhhhhhhhhh...hhhhhh........hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh........hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh......ee.......eeeee.....ee.......eeeeeee....eeeeeeee...hhhhhhhhhhhhhhhhhhhhh..........eee....eeee.....eehhhhhhhh.hhhhhhhhhh....hhhh.hhhhhhhhhhhhhhhhhhhhhh.........eee.....eee....................hhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhh...hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4uwf A 286 LKPNAATRDQLNIIVSYPPTKQLTYEEQDLVWKFRYYLTNQEKALTKFLKCVNWDLPQEAKQALELLGKWKPMDVEDSLELLSSHYTNPTVRRYAVARLRQADDEDLLMYLLQLVQALKYENFDDIKNGLEINSAEIDSSQIITSPLLEQDLCTFLISRACKNSTLANYLYWYVIVECEDQDTQQRDPKTHEMYLNVMRRFSQALLKGDKSVRVMRSLLAAQQTFVDRLVHLMKAVQRESGNRKKKNERLQALLGDNEKMNLSDVELIPLPLEPQVKIRGIIPETATLFKSALMPAQLFFKTEDGGKYPVIFKHGDDLRQDQLILQIISLMDKLLRKENLDLKLTPYKVLATSTKHGFMQFIQSVPVAEVLDTEGSIQNFFRKYAPSENGPNGISAEVMDTYVKSCAGYCVITYILGVGDRHLDNLLLTKTGKLFHIDFGYILGRDPKPLPPPMKLNKEMVEGMGGTQSEQYQEFRKQCYTAFLHLRRYSNLILNLFSLMVDANIPDIALEPDKTVKKVQDKFRLDLSDEEAVHYMQSLIDESVHALFAA 873
                                   295       305       315       325       335       345       355       365       375       385       395       405       415||     443      |473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803       813       823       833       843       853       863       873
                                                                                                                                                            416|            450|                                                                                                                                                                                                                                                                                                                                                                                                                  
                                                                                                                                                             435             471
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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 4UWF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (40, 40)

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        PK3C3_HUMAN | Q8NEB9: 3ihy 3ls8 4oys 4ph4 4uwg 4uwh 4uwk 4uwl 5anl 5enn

(-) Related Entries Specified in the PDB File

4uwg 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