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(-) Description

Title :  P110DELTA/P85ALPHA WITH GDC-0326
 
Authors :  T. P. Heffron, R. A. Heald, C. Ndubaku, B. Q. Wei, M. Augustin, S. Do, K. Ed C. Eigenbrot, L. Friedman, E. Gancia, P. S. Jackson, G. Jones, A. Koles L. B. Lee, J. D. Lesnick, C. Lewis, N. Mclean, M. Mortle, J. Nonomiya, J. S. Price, W. W. Prior, L. Salphati, S. Sideris, S. T. Staben, S. Steinba V. Tsui, J. Wallin, D. Sampath, A. Olivero
Date :  23 Sep 15  (Deposition) - 27 Jan 16  (Release) - 24 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.64
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Lipid Kinase, Inhibitor, Transferase-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. P. Heffron, R. A. Heald, C. Ndubaku, B. Wei, M. Augistin, S. Do, K. Edgar, C. Eigenbrot, L. Friedman, E. Gancia, P. S. Jackson, G. Jones A. Kolesnikov, L. B. Lee, J. D. Lesnick, C. Lewis, N. Mclean, M. Mortl, J. Nonomiya, J. Pang, S. Price, W. W. Prior, L. Salphati, S. Sideris, S. T. Staben, S. Steinbacher, V. Tsui, J. Wallin, D. Sampath, A. G. Olivero
The Rational Design Of Selective Benzoxazepin Inhibitors Of The Alpha-Isoform Of Phosphoinositide 3-Kinase Culminating In The Identification Of (S)-2-((2-(1-Isopropyl-1H-1, 2, 4-Triazol-5-Yl)-5, 6-Dihydrobenzo[F]Imidazo[1, 2-D][1, 4]Oxazepin-9-Yl)Oxy) Propanamide (Gdc-0326).
J. Med. Chem. V. 59 985 2016
PubMed-ID: 26741947  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.5B01483

(-) Compounds

Molecule 1 - PHOSPHATIDYLINOSITOL 4,5-BISPHOSPHATE 3-KINASE CATALYTIC SUBUNIT DELTA ISOFORM
    Chains: A
    EC Number: 2.7.1.153
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Taxid: 7108
    Gene: PIK3CD
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PTDINS-3-KINASE SUBUNIT DELTA,PHOSPHATIDYLINOSITOL 4,5- BISPHOSPHATE 3-KINASE 110 KDA CATALYTIC SUBUNIT DELTA,P110DELTA
 
Molecule 2 - PHOSPHATIDYLINOSITOL 3-KINASE REGULATORY SUBUNIT ALPHA
    Chains: B
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Taxid: 7108
    Fragment: UNP RESIDUES 431-599
    Gene: PIK3R1
    Organism Common: BOVINE
    Organism Scientific: BOS TAURUS
    Organism Taxid: 9913
    Synonym: PTDINS-3-KINASE REGULATORY SUBUNIT ALPHA, PHOSPHATIDYLINOSITOL 3-KINASE 85 KDA REGULATORY SUBUNIT ALPHA,PTDINS- 3-KINASE REGULATORY SUBUNIT P85-ALPHA

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
15H51Ligand/Ion(2S)-2-({2-[1-(PROPAN-2-YL)-1H-1,2,4-TRIAZOL-5-YL]-5,6-DIHYDROIMIDAZO[1,2-D][1,4]BENZOXAZEPIN-9-YL}OXY)PROPANAMIDE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:758 , TRP A:760 , LYS A:779 , ILE A:825 , GLU A:826 , VAL A:828 , SER A:831 , ASP A:832 , PHE A:908 , ASP A:911binding site for residue 5H5 A 1101

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5DXU)

(-) 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:922
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.....eeeeeee...hhhhhhhhhhhhhh...hhhhh.hhh.eeeeee.....eeee.....hhhhhh....eeeeee...hhhhhhhhhhhhhhhh..hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............eeeee......eee......hhhhhhhhhhh.....hhh.eeeee....eee....hhhhhhhhhhhhhhh...eeeeeehhhhhhhhh.........eeeeeeeeee........eeeeeeeeee..ee.........ee.....eeeeeeeeeee........eeeeeeeee....eeeeeeeee..........eeeeee.ee..........................eeeeee...........hhhhhh......hhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..hhhhhhhhh...hhhhhhhhhhhhhh....hhhhhhhhh.....hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.ee.......ee.ee.....ee.......eeeeee.......eeeeee...hhhhhhhhhhhhhhhhhhhh...........eeeee..eeeee....eeehhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........eeee....eee.................hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5dxu A   17 NQSVVVDFLLPTGVYLNFPVSRNANLSTIKQLLWHRAQYEPLFHMLSGPEAYVFTCINQTAEQQELEDEQRRLCDVQPFLPVLRLVAREGDRVKKLINSQISLLIGKGLHEFDSLCDPEVNDFRAKMCQFCEEAAARRQQLGWEAWLQYSFPLQLEPLPNRALLVNVKFEGSEESFTFQVSTKDVPLALMACALRKKAVEQPEDYTLQVNGRHEYLYGSYPLCQFQYICSCLHSGLTPHLTMVHSSSILAMRDEQSLWSLEQPFRIELIQGSKVNADERMKLVVQAGLFHGNEMLCKTVSSSEVSVCSEPVWKQRLEFDINICDLPRMARLCFALYAVIEKDCPIAWANLMLFDYKDQLKTGERCLYMWPSVPDEKGELLNPTGTVRSNPNTDSAAALLICLPEVAPHPVYYPALEKILELGRHEEEQLQLREILERYEHEKDLVWKLRHEVQEHFPEALARLLLVTKWNKHEDVAQMLYLLCSWPELPVLSALELLDFSFPDCHVGSFAIKSLRKLTDDELFQYLLQLVQVLKYESYLDCELTKFLLDRALANRKIGHFLFWHLRSEMHVPSVALRFGLILEAYCRGSTHHMKVLMKQGEALSKLKALNDFVKLSSQKTPKPQTKELMHLCMRQEAYLEALSHLQSPLDPSTLLAEVCVEQCTFMDSKMKPLWIMYSNEEAGSVGIIFKNGDDLRQDMLTLQMIQLMDVLWKQEGLDLRMTPYGCLPTGDRTGLIEVVLRSDTIANIQLNDALLNWLKSKNPGEALDRAIEEFTLSCAGYCVATYVLGIGDRHSDNIMIRESGQLFHIDFGHFLGNFERVPFILTYDFVHVIQQGKTNNSEKFERFRGYCERAYTILRRHGLLFLHLFALMRAAGLPELSCSKDIQYLKDSLALGKTEEEALKHFRVKFNEALRESWKTKV 1031
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166      |187       197       207       217       234       244       254       264       274       284    || 319       329       339       349       359       369       379       389       399||     423       433       443       453       463       473       483       493   ||  510      |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 ||    779       789       799       809       819       829       839||     861       871       881       891       901       911       929       939       949       959       969       979       989       999      1009      1019      1029  
                                                                                                                                                                                      173|                                     225|                                                     289|                                                                                  400|                                                                               497|         517|                                                                                                                                                                                                                                                 768|                                                                 840|                                                               919|                                                                                                       
                                                                                                                                                                                       185                                      233                                                      315                                                                                   415                                                                                505          524                                                                                                                                                                                                                                                  772                                                                  853                                                                928                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:169
                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5dxu B  431 YQQDQVVKEDNIEAVGKKLHEYNTQFQEKSREYDRLYEDYTRTSQEIQMKRTAIEAFNETIKIFEEQCQTQERYSKEYIEKFKREGNETEIQRIMHNYEKLKSRISEIVDSRRRLEEDLKKQAAEYREIDKRMNSIKPDLIQLRKTRDQYLMWLTQKGVRQKKLNEWLG  599
                                   440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590
   Legend:   → Mismatch (orange background)
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  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 5DXU)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (97, 106)

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  5dxu
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  P85A_BOVIN | P23727
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  2.7.1.153
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        P85A_BOVIN | P23727: 1bfi 1bfj 1oo3 1oo4 1pnj 1qad 2pna 2pnb 2pni 5dxh 5t8f
        PK3CD_HUMAN | O00329: 5m6u 5t8f 5ubt 5vlr

(-) Related Entries Specified in the PDB File

5dxh 5dxt