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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 :  2.70
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  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1RBQ1Ligand/Ion(8S)-2-(MORPHOLIN-4-YL)-9-[2-(PROPAN-2-YLOXY)ETHYL]-8-(TRIFLUOROMETHYL)-6,7,8,9-TETRAHYDRO-4H-PYRIMIDO[1,2-A]PYRIMIDIN-4-ONE
2SO43Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:754 , LYS A:756BINDING SITE FOR RESIDUE SO4 A1870
2AC2SOFTWAREARG A:385 , ARG A:482 , LYS A:485BINDING SITE FOR RESIDUE SO4 A1871
3AC3SOFTWARELEU A:393 , TYR A:492 , TYR A:496BINDING SITE FOR RESIDUE SO4 A1872
4AC4SOFTWAREPHE 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 , ILE A:760 , HOH A:2038BINDING SITE FOR RESIDUE RBQ A1873

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4UWG)

(-) 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:544
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh.......hhhhhhhhhhh..hhhhh..hhhhhhh.....hhhhhhhhhhhhhhh...hhhhhhhhhh....hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhh.........hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh......eee..eeeeeeeee.....ee.......eeeeeee....eeeeeeee...hhhhhhhhhhhhhhhhhhhhh..........eee....eeeee....eehhhhhhhhhhhhhhhhhhh....hhhh.hhhhhhhhhhhhhhhhhhhhhhh........eee.....eee....................hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4uwg A 286 LKPNAATRDQLNIIVSYPPTKQLTYEEQDLVWKFRYYLTNQEKALTKFLKCVNWDLPQEAKQALELLGKWKPMDVEDSLELLSSHYTNPTVRRYAVARLRQADDEDLLMYLLQLVQALKYENFDDIKNGLEAEIDSSQIITSPLPLEQDLCTFLISRACKNSTLANYLYWYVIVECEDQDTQQRDPKTHEMYLNVMRRFSQALLKGDKSVRVMRSLLAAQQTFVDRLVHLMKAVQRESGNRKKKNERLQALLGDNEKMNLSDVELIPLPLEPQVKIRGIIPETATLFKSALMPAQLFFKTEDGGKYPVIFKHGDDLRQDQLILQIISLMDKLLRKENLDLKLTPYKVLATSTKHGFMQFIQSVPVAEVLDTEGSIQNFFRKYAPSENGPNGISAEVMDTYVKSCAGYCVITYILGVGDRHLDNLLLTKTGKLFHIDFGYILGRDPKPLPPPMKLNKEMVEGMGGTQSEQYQEFRKQCYTAFLHLRRYSNLILNLFSLMVDANIPDIALEPDKTVKKVQDKFRLDLSDEEAVHYMQSLIDESVHA 869
                                   295       305       315       325       335       345       355       365       375       385       395       405       415||     446    || 475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795       805       815       825       835       845       855       865    
                                                                                                                                                            416|          451|                                                                                                                                                                                                                                                                                                                                                                                                              
                                                                                                                                                             438           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 4UWG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (40, 40)

Asymmetric/Biological Unit(hide GO term definitions)

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

(-) Related Entries Specified in the PDB File

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