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(-) Description

Title :  CRYSTAL STRUCTURE OF A NOVEL TETRAHYDROPYRAZOLO[1,5-A]PYRAZINE IN AN ENGINEERED PI3K ALPHA
 
Authors :  M. S. Knapp, R. A. Elling
Date :  29 Aug 14  (Deposition) - 31 Dec 14  (Release) - 28 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.39
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Pi3K, Chimera, Lipid Kinase, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. A. Barsanti, R. J. Aversa, X. Jin, Y. Pan, Y. Lu, R. Elling, R. Jain, M. Knapp, J. Lan, X. Lin, P. Rudewicz, J. Sim, L. Taricani, G. Thomas, L. Xiao, Q. Yue
Structure-Based Drug Design Of Novel Potent And Selective Tetrahydropyrazolo[1, 5-A]Pyrazines As Atr Inhibitors.
Acs Med. Chem. Lett. V. 6 37 2015
PubMed-ID: 25589927  |  Reference-DOI: 10.1021/ML500353P

(-) Compounds

Molecule 1 - PHOSPHATIDYLINOSITOL 4,5-BISPHOSPHATE 3-KINASE CATALYTIC SUBUNIT ALPHA ISOFORM
    ChainsA
    EC Number2.7.1.153, 2.7.11.1
    EngineeredYES
    Expression SystemTRICHOPLUSIA NI
    Expression System Cell LineTN5
    Expression System Taxid7111
    Expression System Vector TypeBACULOVIRUS
    GenePIK3CA
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPTDINS-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
    ChainsB
    EngineeredYES
    Expression SystemTRICHOPLUSIA NI
    Expression System Cell LineTN5
    Expression System Taxid7111
    Expression System Vector TypeBACULOVIRUS
    FragmentUNP RESIDUES 2-317
    GenePIK3R1, GRB1
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPTDINS-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
13K61Ligand/IonN,N-DIMETHYL-4-[(6R)-6-METHYL-5-(1H-PYRROLO[2,3-B]PYRIDIN-4-YL)-4,5,6,7-TETRAHYDROPYRAZOLO[1,5-A]PYRAZIN-3-YL]BENZENESULFONAMIDE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:780 , MET A:800 , LYS A:802 , ASP A:810 , TYR A:836 , ILE A:848 , GLU A:849 , VAL A:850 , VAL A:851 , SER A:854 , GLN A:859 , MET A:922 , ASP A:933binding site for residue 3K6 A 1101

(-) SS Bonds  (0, 0)

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

(-) 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 4WAF)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4WAF)

(-) 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:1017
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................eeeeeee.....eeeeeee...hhhhhhhhhhhhhhhh.hhhhh.hhhhheeeee.....eeee.....hhhhh.....eeeee....hhhhhhhhhhhhhhhh..hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh..........hhhhhh.....eeeeeeeeee....eeeeeeeeee...hhhhhhhhhhhh.....hhhhhhhh......eeeee.....ee....hhhhhhhhhhhhhhh...eeeeeehhhhhh.........hhhhhh...eee.hhh..eeeeeeeee...........eeeeeeeeee..ee....ee.........eeeeeeeeeee.hhh....eeeeeeeeeeeee..eeeeeeeeeeeee..........eeeeee...........................eeeeee.....eee..hhhhhhhhhhhhh.hhhhhhhhhhhhh......hhhhhhhhhhh..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh....hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh.hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.ee.......ee...hhhhhee.......eeeeee....hhhhh..eeeeeeee...hhhhhhhhhhhhhhhhhhhhh..........eeeee..eeeee....eeehhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeee....eee.........................hhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4waf A    2 PPRPSSGELWGIHLMPPRILVECLLPNGMIVTLECLREATLITIKHELFKEARKYPLHQLLQDESSYIFVSVTQEAEREEFFDETRRLCDLRLFQPFLKVIEPVGNREEKILNREIGFAIGMPVCEFDMVKDPEVQDFRRNILNVCKEAVDLRDLNSPHSRAMYVYPPNVESSPELPKHIYNKLDKGQIIVVIWVIVSPNNDKQKYTLKINHDCVPEQVIAEAIRKKTRLSSEQLKLCVLEYQGKYILKVCGCDEYFLEKYPLSQYKYIRSCIMLGRMPNLMLMAKESLYSQLPMDCFTMPSYSRRISSTKSLWVINSALRIKILCATYVNVNIRDIDKIYVRTGIYHGGEPLCDNVNTQRVPCSNPRWNEWLNYDIYIPDLPRAARLCLSICSVKGRKGAKEEHCPLAWGNINLFDYTDTLVSGKMALNLWPVPHGLEDLLNPIGVTGSNPNKETPCLELEFDWFSSVVKFPDMSVIEEHANWSVRENDKEQLKAISTRDPLSEITEQEKDFLWSHRHYCVTIPEILPKLLLSVKWNSRDEVAQMYCLVKDWPPIKPEQAMELLDCNYPDPMVRGFAVRCLEKYLTDDKLSQYLIQLVQVLKYEQYLDNLLVRFLLKKALTNQRIGHFFFWHLKSEMHNKTVSQRFGLLLESYCRACGMYLKHLNRQVEAMEKLINLTDILKQEKKDETQKVQMKFLVEQMRRPDFMDALQGFLSPLNPAHQLGNLRLEECRIMSSAKRPLWLNWENPDIMSELLFQNNEIMFKNGDDLRQDMLTLQIIRIMENIWQNQGLDLRMLPYGCLSIGDCVGLIEVVRNSHTIMQIQCKGFNSHTLHQWLKDKNKGEIYDAAIDLFTRSCAGYCVATFILGIGDRHNSNIMVKDDGQLVHIDFGHFLDHKKKKFGYKRERVPFVLTQDFLIVISKGAQECTKTREFERFQEMCYKAYLAIRQHANLFINLFSMMLGSGMPELQSFDDIAYIRKTLALDKTEQEALEYFMKQMNDAHHGGWTTKMDWIFHT 1061
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       234       244       254       264       274       284       294       304       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494     ||527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767       777       787       797       807       817       827       837       847       857      |874       884       894       904       914       924       934       944       954       964       974       984       994      1004      1014      1024      1034      1044      1054       
                                                                                                                                                                                                                                                              230|                                                                           312|                                                                                                                                                                              500|                                                                                                                                                                                                                                                                                                                                                 864|                                                                                                                                                                                             
                                                                                                                                                                                                                                                               234                                                                            323                                                                                                                                                                               524                                                                                                                                                                                                                                                                                                                                                  872                                                                                                                                                                                             

Chain B from PDB  Type:PROTEIN  Length:250
                                                                                                                                                                                                                                                                                           
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eee..hhhhhhhhhh......eeeee....eeeeeee..eeeeeee.........hhhhhhhhhhhh...............hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4waf B  325 NMSLQDAEWYWGDISREEVNEKLRDTADGTFLVRDASTDYTLTLRKGGNNKLIKIFFSDPLTFSSVVELINHYRNELAQLDVKLLYPVSKQQDQVVKEDNIEAVGKKLHEYNTQFQEKSREYDRLYEEYTRTSQEIQMKRTAIEAFNETIKIFEEQCQTQERYSKEYIEKFKREGNEKEIQRIMHNYDKLKSRISEIIDSRRRLEEDLKKQAAEYREIDKRMNSIKPDLIQLRKTRDQYLMWLTQKGVRQ  591
                                   334       344       354       368       378     ||395       405     ||420       430|      441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591
                                                               362|              384|                411| ||       430|                                                                                                                                                               
                                                                367               392                 413 ||        432                                                                                                                                                               
                                                                                                        415|                                                                                                                                                                          
                                                                                                         420                                                                                                                                                                          

   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 4WAF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (109, 132)

Asymmetric/Biological Unit(hide GO term definitions)

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  P85A_HUMAN | P27986
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 Related Entries

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

UniProtKB/Swiss-Prot
        P85A_HUMAN | P279861a0n 1azg 1h9o 1pbw 1pht 1pic 1pks 1pkt 2iug 2iuh 2iui 2rd0 2v1y 3hhm 3hiz 3i5r 3i5s 4a55 4jps 4l1b 4l23 4l2y 4ovu 4ovv 4ykn 4zop 5aul 5fi4 5gji 5itd 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 | P423362enq 2rd0 3hhm 3hiz 3zim 4jps 4l1b 4l23 4l2y 4ovu 4ovv 4tuu 4tv3 4ykn 4zop 5dxh 5dxt 5fi4 5itd 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

(no "Related Entries Specified in the PDB File" available for 4WAF)