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(-) Description

Title :  THE CRYSTAL STRUCTURE OF HUMAN VPS34 IN COMPLEX WITH A SELECTIVE AND POTENT INHIBITOR
 
Authors :  E. P. Kearney
Date :  09 Nov 15  (Deposition) - 16 Nov 16  (Release) - 16 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Vps34, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. P. Kearney
Potent, Selective, And Orally Bioavailable Inhibitors Of Vps34 Provide Chemical Tools To Modulate Autophagy In Vivo
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PHOSPHATIDYLINOSITOL 3-KINASE CATALYTIC SUBUNIT TYPE 3
    Chains: A, B
    EC Number: 2.7.1.137
    Engineered: YES
    Expression System: UNIDENTIFIED BACULOVIRUS
    Expression System Taxid: 10469
    Fragment: UNP RESIDUES 293-887
    Gene: PIK3C3, VPS34
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PTDINS-3-KINASE TYPE 3,PHOSPHATIDYLINOSITOL 3-KINASE P100 SUBUNIT,PHOSPHOINOSITIDE-3-KINASE CLASS 3,HVPS34

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric Unit (4, 6)
No.NameCountTypeFull Name
15QS2Ligand/Ion1-[[4-(CYCLOPROPYLMETHYL)-5-[2-(PYRIDIN-4-YLAMINO)PYRIMIDIN-4-YL]PYRIMIDIN-2-YL]AMINO]-2-METHYL-PROPAN-2-OL
2GOL1Ligand/IonGLYCEROL
3NA2Ligand/IonSODIUM ION
4SO41Ligand/IonSULFATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
15QS1Ligand/Ion1-[[4-(CYCLOPROPYLMETHYL)-5-[2-(PYRIDIN-4-YLAMINO)PYRIMIDIN-4-YL]PYRIMIDIN-2-YL]AMINO]-2-METHYL-PROPAN-2-OL
2GOL-1Ligand/IonGLYCEROL
3NA-1Ligand/IonSODIUM ION
4SO4-1Ligand/IonSULFATE ION
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
15QS1Ligand/Ion1-[[4-(CYCLOPROPYLMETHYL)-5-[2-(PYRIDIN-4-YLAMINO)PYRIMIDIN-4-YL]PYRIMIDIN-2-YL]AMINO]-2-METHYL-PROPAN-2-OL
2GOL1Ligand/IonGLYCEROL
3NA-1Ligand/IonSODIUM ION
4SO41Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:612 , SER A:614 , 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:1002 , HOH A:1057 , HOH A:1077binding site for residue 5QS A 901
2AC2SOFTWAREPRO A:669binding site for residue NA A 902
3AC3SOFTWAREPHE B:612 , ILE B:634 , LYS B:636 , MET B:682 , GLN B:683 , PHE B:684 , ILE B:685 , SER B:687 , LEU B:750 , ILE B:760 , ASP B:761 , HOH B:1001 , HOH B:1032 , HOH B:1091binding site for residue 5QS B 901
4AC4SOFTWARETHR B:668 , PRO B:669 , GLN B:683 , ILE B:685 , LYS B:756 , HOH B:1039binding site for residue GOL B 903
5AC5SOFTWARETYR B:494 , SER B:525 , ARG B:539 , HOH B:1082binding site for residue SO4 B 904

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5ENN)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5ENN)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5ENN)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5ENN)

(-) Exons   (0, 0)

(no "Exon" information available for 5ENN)

(-) Sequences/Alignments

Asymmetric 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:526
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh......hhhhhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhhhhhhhh...hhhhhhhhhh....hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh...........eee..eeeeeeeee.....ee.......eeeeeee....eeeeeeee...hhhhhhhhhhhhhhhhhhhhh..........eee....eeeee....eehhhhhhhh.hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh.........eee.....eee....................hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5enn A 293 RDQLNIIVSYPPTKQLTYEEQDLVWKFRYYLTNQEKALTKFLKCVNWDLPQEAKQALELLGKWKPMDVEDSLELLSSHYTNPTVRRYAVARLRQADDEDLLMYLLQLVQALKYENFDDIKNGLELEQDLCTFLISRACKNSTLANYLYWYVIVECEDQDTQQRDPKTHEMYLNVMRRFSQALLKGDKSVRVMRSLLAAQQTFVDRLVHLMKAVQRESGNRKKKNERLQALLGDNEKMNLSDVELIPLPLEPQVKIRGIIPETATLFKSALMPAQLFFKTEDGGKYPVIFKHGDDLRQDQLILQIISLMDKLLRKENLDLKLTPYKVLATSTKHGFMQFIQSVPVAEVLDTEGSIQNFFRKYAPSENGPNGISAEVMDTYVKSCAGYCVITYILGVGDRHLDNLLLTKTGKLFHIDFGYILGRDPKPLPPPMKLNKEMVEGMGGTQSEQYQEFRKQCYTAFLHLRRYSNLILNLFSLMVDANIPDIALEPDKTVKKVQDKFRLDLSDEEAVHYMQSLIDESVHALFA 872
                                   302       312       322       332       342       352       362       372       382       392       402       412   ||  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|                                                                                                                                                                                                                                                                                                                                                                                                                 
                                                                                                                                                      471                                                                                                                                                                                                                                                                                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:531
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh......hhhhhhhhhhhhhhhh....hhhhhhhhh...hhhhhhhhhhhhhhh...hhhhhhhhhh....hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh...........eee..eeeeeeeee.....ee.......eeeeeee....eeeeeeee...hhhhhhhhhhhhhhhhhhhhh..........eee....eeeee....eehhhhhhhh.hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh.........eee.....eee....................hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5enn B 288 MGSGIRDQLNIIVSYPPTKQLTYEEQDLVWKFRYYLTNQEKALTKFLKCVNWDLPQEAKQALELLGKWKPMDVEDSLELLSSHYTNPTVRRYAVARLRQADDEDLLMYLLQLVQALKYENFDDIKNGLEPLEQDLCTFLISRACKNSTLANYLYWYVIVECEDQDTQQRDPKTHEMYLNVMRRFSQALLKGDKSVRVMRSLLAAQQTFVDRLVHLMKAVQRESGNRKKKNERLQALLGDNEKMNLSDVELIPLPLEPQVKIRGIIPETATLFKSALMPAQLFFKTEDGGKYPVIFKHGDDLRQDQLILQIISLMDKLLRKENLDLKLTPYKVLATSTKHGFMQFIQSVPVAEVLDTEGSIQNFFRKYAPSENGPNGISAEVMDTYVKSCAGYCVITYILGVGDRHLDNLLLTKTGKLFHIDFGYILGRDPKPLPPPMKLNKEMVEGMGGTQSEQYQEFRKQCYTAFLHLRRYSNLILNLFSLMVDANIPDIALEPDKTVKKVQDKFRLDLSDEEAVHYMQSLIDESVHALF 871
                                   297       307       317       327       337       347       357       367       377       387       397       407       417|      480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860       870 
                                                                                                                                                           417|                                                                                                                                                                                                                                                                                                                                                                                                                
                                                                                                                                                            471
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  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 5ENN)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5ENN)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5ENN)

(-) Gene Ontology  (40, 40)

Asymmetric Unit(hide GO term definitions)

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

(-) Related Entries Specified in the PDB File

4ph4 SAME PROTEIN DIFFERENT LIGAND