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(-) Description

Title :  CRYSTAL STRUCTURE OF PI3K ALPHA WITH PI3K DELTA INHIBITOR
 
Authors :  M. S. Knapp, R. A. Elling
Date :  16 Mar 16  (Deposition) - 07 Sep 16  (Release) - 07 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.02
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Inhibitor, Lipid Kinase, Pi3K, Alpha, Delta, Transferase-Protein Transport-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Hoegenauer, N. Soldermann, F. Stauffer, P. Furet, N. Graveleau, A. B. Smith, C. Hebach, G. J. Hollingworth, I. Lewis, S. Gutmann, G. Rummel, M. Knapp, R. M. Wolf, J. Blanz, R. Feifel, C. Burkhart, F. Zecri
Discovery And Pharmacological Characterization Of Novel Quinazoline-Based Pi3K Delta-Selective Inhibitors.
Acs Med. Chem. Lett. V. 7 762 2016
PubMed-ID: 27563400  |  Reference-DOI: 10.1021/ACSMEDCHEMLETT.6B00119

(-) Compounds

Molecule 1 - PHOSPHATIDYLINOSITOL 4,5-BISPHOSPHATE 3-KINASE CATALYTIC SUBUNIT ALPHA ISOFORM
    Chains: A
    EC Number: 2.7.1.153, 2.7.11.1
    Engineered: YES
    Expression System: UNIDENTIFIED BACULOVIRUS
    Expression System Cell Line: TN5
    Expression System Taxid: 10469
    Gene: PIK3CA
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PTDINS-3-KINASE SUBUNIT ALPHA,PHOSPHATIDYLINOSITOL 4,5- BISPHOSPHATE 3-KINASE 110 KDA CATALYTIC SUBUNIT ALPHA,P110ALPHA, PHOSPHOINOSITIDE-3-KINASE CATALYTIC ALPHA POLYPEPTIDE, SERINE/THREONINE PROTEIN KINASE PIK3CA
 
Molecule 2 - PHOSPHATIDYLINOSITOL 3-KINASE REGULATORY SUBUNIT ALPHA
    Chains: B
    Engineered: YES
    Expression System: UNIDENTIFIED BACULOVIRUS
    Expression System Cell: TN5
    Expression System Taxid: 10469
    Fragment: UNP RESIDUES 2-317
    Gene: PIK3R1, GRB1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    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
16CY1Ligand/Ion5-{4-[3-(4-ACETYLPIPERAZINE-1-CARBONYL)PHENYL]QUINAZOLIN-6-YL}-2-METHOXYPYRIDINE-3-CARBONITRILE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:802 , TYR A:836 , ILE A:848 , GLU A:849 , VAL A:851 , SER A:854 , GLN A:859 , MET A:922 , ILE A:932 , HOH A:1203binding site for residue 6CY A 1101

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ser A:158 -Pro A:159
2Ser A:199 -Pro A:200

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5ITD)

(-) 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:995
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................eeeeeee.....eeeeeee...hhhhhhhhhhhhhh...hhhhh.hhhhheeeee.....eee......hhhhh.....eeeee....hhhhhhhhhhhhhhhh..hhhhhh..hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhh..........hhhhhh.....eeeeeeeeee....eeeeeeeeee...hhhhhhhhhhhh.....eeeee.....ee....hhhhhhhhhhhhhhh...eeeeeehhhhhh.........hhhhhh..eee.hhh..eeeeeeeee...........eeeeeeeeee..ee....ee.........eeeeeeeeeee.hhh....eeeeeeeeee.......eeeeeeeeeee..........eeeeee...........................eeeeee.....eee..hhhhhh.....hhhhhhhhhhh.......hhhhhhhhhhh..hhhhhhhhhhhhhh.....hhhhhhhhhhhhhh....hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh.hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.eee..eeeeee...hhhhhee.......eeeeee....hhhhh..eeeeeeee...hhhhhhhhhhhhhhhhhhhhh..........eeeee..eeeee....eeehhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeee....eee.........hhhhhh..........hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5itd A    2 PPRPSSGELWGIHLMPPRILVECLLPNGMIVTLECLREATLITIKHELFKEARKYPLHQLLQDESSYIFVSVTQEAEREEFFDETRRLCDLRLFQPFLKVIEPVGNREEKILNREIGFAIGMPVCEFDMVKDPEVQDFRRNILNVCKEAVDLRDLNSPHSRAMYVYPPNVESSPELPKHIYNKLDKGQIIVVIWVIVSPNNDKQKYTLKINHDCVPEQVIAEAIRKEYQGKYILKVCGCDEYFLEKYPLSQYKYIRSCIMLGRMPNLMLMAKESLYSQLPMDCFTMPSYSRRISTKSLWVINSALRIKILCATYVNVNIRDIDKIYVRTGIYHGGEPLCDNVNTQRVPCSNPRWNEWLNYDIYIPDLPRAARLCLSICSVKGRKGAKEEHCPLAWGNINLFDYTDTLVSGKMALNLWPVPHGLEDLLNPIGVTGSNPNKETPCLELEFDWFSSVVKFPDMSVIEEHANENDKEQLKAISTRDPLSEITEQEKDFLWSHRHYCVTIPEILPKLLLSVKWNSRDEVAQMYCLVKDWPPIKPEQAMELLDCNYPDPMVRGFAVRCLEKYLTDDKLSQYLIQLVQVLKYEQYLDNLLVRFLLKKALTNQRIGHFFFWHLKSEMHNKTVSQRFGLLLESYCRACGMYLKHLNRQVEAMEKLINLTDILKQEKKDETQKVQMKFLVEQMRRPDFMDALQGFLSPLNPAHQLGNLRLEECRIMSSAKRPLWLNWENPDIMSELLFQNNEIIFKNGDDLRQDMLTLQIIRIMENIWQNQGLDLRMLPYGCLSIGDCVGLIEVVRNSHTIMQIQCKFNSHTLHQWLKDKNKGEIYDAAIDLFTRSCAGYCVATFILGIGDRHNSNIMVKDDGQLFHIDFGHFLDHKKKKFGYKRERVPFVLTQDFLIVISKGAQECTKTREFERFQEMCYKAYLAIRQHANLFINLFSMMLGSGMPELQSFDDIAYIRKTLALDKTEQEALEYFMKQMNDAHHGGWTTKMDWIF 1059
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221     ||248       258       268       278       288       298       308  ||   329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       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      |874       884       894       904       914       924       934       944       954       964       974       984       994      1004      1014      1024      1034      1044      1054     
                                                                                                                                                                                                                                                           227|                                                               311|                                                                                                                                                                           497|                                                                                                                                                                                                                                                                                                                                               863|                                                                                                                                                                                           
                                                                                                                                                                                                                                                            245                                                                323                                                                                                                                                                            525                                                                                                                                                                                                                                                                                                                                                872                                                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:237
                                                                                                                                                                                                                                                                              
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh..eee..hhhhhhhhhh......eeeee....eeeeeee..eeeeeee........hhhhhhhh................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5itd B  327 SLQDAEWYWGDISREEVNEKLRDTADGTFLVRDASTDYTLTLRKGGNNKLIKIFSDPLTFSSVVELINHYRLLYPVSKDQVVKEDNIEAVGKKLHEYNTQFQEKSREYDRLYEEYTRTSQEIQMKRTAIEAFNETIKIFEEQCQTQERYSKEYIEKFKREGNEKEIQRIMHNYDKLKSRISEIIDSRRRLEEDLKKQAAEYREIDKRMNSIKPDLIQLRKTRDQYLMWLTQKGVRQK  592
                                   336       346       356     ||370       380  ||   398       408||     435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       
                                                             362|             383|              409|   430|                                                                                                                                                              
                                                              367              392               424    434
   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 5ITD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (109, 132)

Asymmetric/Biological Unit(hide GO term definitions)

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  5itd
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  P85A_HUMAN | P27986
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  PK3CA_HUMAN | P42336
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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_HUMAN | P27986: 1a0n 1azg 1h9o 1pbw 1pht 1pic 1pks 1pkt 2iug 2iuh 2iui 2rd0 2v1y 3hhm 3hiz 3i5r 3i5s 4a55 4jps 4l1b 4l23 4l2y 4ovu 4ovv 4waf 4ykn 4zop 5aul 5fi4 5gji 5m6u 5sw8 5swg 5swo 5swp 5swr 5swt 5sx8 5sx9 5sxa 5sxb 5sxc 5sxd 5sxe 5sxf 5sxi 5sxj 5sxk 5ubt 5uk8 5ukj 5ul1 5vlr
        PK3CA_HUMAN | P42336: 2enq 2rd0 3hhm 3hiz 3zim 4jps 4l1b 4l23 4l2y 4ovu 4ovv 4tuu 4tv3 4waf 4ykn 4zop 5dxh 5dxt 5fi4 5sw8 5swg 5swo 5swp 5swr 5swt 5sx8 5sx9 5sxa 5sxb 5sxc 5sxd 5sxe 5sxf 5sxi 5sxj 5sxk 5ubr 5uk8 5ukj 5ul1

(-) Related Entries Specified in the PDB File

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