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(-) Description

Title :  THE CO-STRUCTURE OF (R)-4-(6-(1-(CYCLOPROPYLSULFONYL)CYCLOPROPYL)-2-(1H-INDOL-4-YL)PYRIMIDIN-4-YL)-3-METHYLMORPHOLINE AND A RATIONALLY DESIGNED PI3K-ALPHA MUTANT THAT MIMICS ATR
 
Authors :  M. S. Knapp, M. Mamo, R. A. Elling
Date :  20 Jan 17  (Deposition) - 14 Jun 17  (Release) - 14 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Inhibitor, Lipid Kinase, Mutation, Atr, Transferase-Signaling Protein-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Lu, M. Knapp, K. Crawford, R. Warne, R. Elling, K. Yan, M. Doyle, G. Pardee, L. Zhang, S. Ma, M. Mamo, E. Ornelas, Y. Pan, D. Bussiere, J. Jansen, I. Zaror, A. Lai, P. Barsanti, J. Sim
Rationally Designed Pi3K Alpha Mutants To Mimic Atr And Their Use To Understand Binding Specificity Of Atr Inhibitors.
J. Mol. Biol. V. 429 1684 2017
PubMed-ID: 28433539  |  Reference-DOI: 10.1016/J.JMB.2017.04.006

(-) 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 Taxid: 10469
    Gene: PIK3CA
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: POINT MUTATION TO THE BINDING POCKET OF P110 PI3K ALPHA DESIGNED TO MIMIC ATR LIGAND BINDING PROPERTIES.
    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 Taxid: 10469
    Gene: PIK3R1, GRB1
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: FRAGMENT OF WILD TYPE P85
    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
18DV1Ligand/Ion(R)-4-(6-(1-(CYCLOPROPYLSULFONYL)CYCLOPROPYL)-2-(1H-INDOL-4-YL)PYRIMIDIN-4-YL)-3-METHYLMORPHOLINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:311 , SER A:774 , PRO A:778 , LYS A:802 , ASP A:810 , TYR A:836 , ILE A:848 , GLU A:849 , TRP A:850 , VAL A:851 , SER A:854 , THR A:856 , MET A:922 , ILE A:932 , ASP A:933binding site for residue 8DV A 1101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5UK8)

(-) 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 5UK8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5UK8)

(-) Exons   (0, 0)

(no "Exon" information available for 5UK8)

(-) 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:1008
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .................eeeeeee.....eeeeeee...hhhhhhhhhhhhhhhh.hhhhh.hhhhheeeee.....eeee.....hhhhhh....eeeee....hhhhhhhhhhhhhhhh..hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh..........hhhhhh.....eeeeeeeeee....eeeeeeeeee...hhhhhhhhhhhh................eeee.....ee....hhhhhhhhhhhhhhh...eeeeehhhhhhh.........hhhhh.....eee.hhh..eeeeeeeee...........eeeeeeeeee..ee....ee.........eeeeeeeeeee.hhh....eeeeeeeeeeeee..eeeeeeeeeeeee...........eeeee...........................eeeee......eee..hhhhhhhhhh...hhhhhhhhhhhhh......hhhhhhhhhhh.hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh...hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh.hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh..eee..eeeeee...hhhhhee.......eeeeee....hhhhh..eeeeeeee...hhhhhhhhhhhhhhhhhhhhh..........eeeee..eeeee....eeehhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeee....eee.......hhhhhhhh..........hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5uk8 A    2 PPRPSSGELWGIHLMPPRILVECLLPNGMIVTLECLREATLITIKHELFKEARKYPLHQLLQDESSYIFVSVTQEAEREEFFDETRRLCDLRLFQPFLKVIEPVGNREEKILNREIGFAIGMPVCEFDMVKDPEVQDFRRNILNVCKEAVDLRDLNSPHSRAMYVYPPNVESSPELPKHIYNKLDKGQIIVVIWVIVSPNNDKQKYTLKINHDCVPEQVIAEAIRKKTRQLKLCVLEYQGKYILKVCGCDEYFLEKYPLSQYKYIRSCIMLGRMPNLMLMAKESLYSQLPMDCFTMPSYSRRISTSTKSLWVINSALRIKILCATYVNVNIRDIDKIYVRTGIYHGGEPLCDNVNTQRVPCSNPRWNEWLNYDIYIPDLPRAARLCLSICSVKGRKGAKEEHCPLAWGNINLFDYTDTLVSGKMALNLWPVPHGLEDLLNPIGVTGSNPNKETPCLELEFDWFSSVVKFPDMSVIEEHANWSRENDKEQLKAISTRDPLSEITEQEKDFLWSHRHYCVTIPEILPKLLLSVKWNSRDEVAQMYCLVKDWPPIKPEQAMELLDCNYPDPMVRGFAVRCLEKYLTDDKLSQYLIQLVQVLKYEQYLDNLLVRFLLKKALTNQRIGHFFFWHLKSEMHNKTVSQRFGLLLESYCRACGMYLKHLNRQVEAMEKLINLTDILKQEKKDETQKVQMKFLVEQMRRPDFMDALQGFLSPLNPAHQLGNLRLEECEIMSSAKRPLKLNWENPDIMSELLFQNNIIMFKNGDDLRQDMLTLQIIRIMENIWQNQGLDLRMLPYGCLSIGDCVGLIEWVRNSHTIMQIQCKFNSHTLHQWLKDKNKGEIYDAAIDLFTRSCAGYCVATFILGIGDRHNSNIMVKDDGQLVHIDFGHFLDHKKKKFGYKRERVPFVLTQDFLIVISKGAQECTKTREFERFQEMCYKAYLAIRQHANLFINLFSMMLGSGMPELQSFDDIAYIRKTLALDKTEQEALEYFMKQMNDAHHGGWTTKMDW 1057
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       238       248       258       268       278       288       298       308    || 327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497 ||    531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861 ||    879       889       899       909       919       929       939       949       959       969       979       989       999      1009      1019      1029      1039      1049        
                                                                                                                                                                                                                                                              230|                                                                        313|                                                                                                                                                                             499|                                                                                                                                                                                                                                                                                                                                                863|                                                                                                                                                                                         
                                                                                                                                                                                                                                                               238                                                                         323                                                                                                                                                                              524                                                                                                                                                                                                                                                                                                                                                 872                                                                                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:244
                                                                                                                                                                                                                                                                                     
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee..hhhhhhhhh......eeeeee.....eeeeeee..eeeeeee............hhhhhhhhhh....ee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5uk8 B  326 MSLQDAEWYWGDISREEVNEKLRDTADGTFLVRDASTGDYTLTLRKGGNNKLIKIFHRDFSDPLTFSSVVELINHYRVKLLYPVSKYQQKEDNIEAVGKKLHEYNTQFQEKSREYDRLYEEYTRTSQEIQMKRTAIEAFNETIKIFEEQCQTQERYSKEYIEKFKREGNEKEIQRIMHNYDKLKSRISEIIDSRRRLEEDLKKQAAEYREIDKRMNSIKPDLIQLRKTRDQYLMWLTQKGVRQK  592
                                   335       345       355      |368       378       392       402      |424       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588    
                                                              362|                  387|              409|        433|                                                                                                                                                          
                                                               366                   392               422         438
   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 5UK8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5UK8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5UK8)

(-) Gene Ontology  (109, 132)

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  PK3CA_HUMAN | P42336
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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 5itd 5m6u 5sw8 5swg 5swo 5swp 5swr 5swt 5sx8 5sx9 5sxa 5sxb 5sxc 5sxd 5sxe 5sxf 5sxi 5sxj 5sxk 5ubt 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 5itd 5sw8 5swg 5swo 5swp 5swr 5swt 5sx8 5sx9 5sxa 5sxb 5sxc 5sxd 5sxe 5sxf 5sxi 5sxj 5sxk 5ubr 5ukj 5ul1

(-) Related Entries Specified in the PDB File

5ukj 5ul1