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(-) Description

Title :  THE CO-STRUCTURE OF 3-AMINO-6-(4-((1-(DIMETHYLAMINO)PROPAN-2-YL) SULFONYL)PHENYL)-N-PHENYLPYRAZINE-2-CARBOXAMIDE AND A RATIONALLY DESIGNED PI3K-ALPHA MUTANT THAT MIMICS ATR
 
Authors :  M. S. Knapp, R. A. Elling, M. Mamo
Date :  23 Jan 17  (Deposition) - 10 May 17  (Release) - 14 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
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
    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
    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
18DY1Ligand/Ion3-AMINO-6-(4-{[(2S)-1-(DIMETHYLAMINO)PROPAN-2-YL]SULFONYL}PHENYL)-N-PHENYLPYRAZINE-2-CARBOXAMIDE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:311 , LYS A:802 , TYR A:836 , ILE A:848 , GLU A:849 , TRP A:850 , VAL A:851 , SER A:854 , HIS A:855 , THR A:856 , GLN A:859 , MET A:922 , ILE A:932 , ASP A:933binding site for residue 8DY A 1101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5UL1)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ser A:199 -Pro A:200
2Asp B:394 -Pro B:395

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5UL1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5UL1)

(-) Exons   (0, 0)

(no "Exon" information available for 5UL1)

(-) 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:1000
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................eeeeeee.....eeeeeee...hhhhhhhhhhhhh....hhhhh.hhhhheeeee.....eeee.....hhhhh.....eeeee....hhhhhhhhhhhhhhhh..hhhhhh..hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh..........hhhhhhhhhh.eeeeeeee.........eeeeeee...hhhhhhhhhhhhhh..hhhhhhhhh...eeee...........hhhhhhhhhhhhhh....eeeee.hhhhhh.........hhhhhh..ee.hhh..eeeeeeeee...........eeeeeeeeee..ee....ee.........eeeeeeeeeee.hhh....eeeeeeeeee.......eeeeeeeeeee..........eeeeee...........................eeeeee......ee..hhhhhhhhhhhhh.hhhhhhhhhhhhh......hhhhhhhhhhh.hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh....hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.ee.......ee...hhhhhee.......eeeeee....hhhhh..eeeeeeee...hhhhhhhhhhhhhhhhhhhhh..........eeeee..eeeee....eeehhhhh...hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh........eeee....eee.........................hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5ul1 A    2 PPRPSSGELWGIHLMPPRILVECLLPNGMIVTLECLREATLITIKHELFKEARKYPLHQLLQDESSYIFVSVTQEAEREEFFDETRRLCDLRLFQPFLKVIEPVGNREEKILNREIGFAIGMPVCEFDMVKDPEVQDFRRNILNVCKEAVDLRDLNSPHSRAMYVYPPNVESSPELPKHIYNKLDKGQIIVVIWVIVSPNNDKQKYTLKINHDCVPEQVIAEAIRKKTEQLKLCVLEYQGKYILKVCGCDEYFLEKYPLSQYKYIRSCIMLGRMPNLMLMAKESLYSQLPMDCFTMPSYSRRITKSLWVINSALRIKILCATYVNVNIRDIDKIYVRTGIYHGGEPLCDNVNTQRVPCSNPRWNEWLNYDIYIPDLPRAARLCLSICSVKGRKGAKEEHCPLAWGNINLFDYTDTLVSGKMALNLWPVPHGLEDLLNPIGVTGSNPNKETPCLELEFDWFSSVVKFPDMSVIEEHANWSVRENDKEQLKAISTRDPLSEITEQEKDFLWSHRHYCVTIPEILPKLLLSVKWNSRDEVAQMYCLVKDWPPIKPEQAMELLDCNYPDPMVRGFAVRCLEKYLTDDKLSQYLIQLVQVLKYEQYLDNLLVRFLLKKALTNQRIGHFFFWHLKSEMHNKTVSQRFGLLLESYCRACGMYLKHLNRQVEAMEKLINLTDILKQEKKDETQKVQMKFLVEQMRRPDFMDALQGFLSPLNPAHQLGNLRLEECEIMSSAKRPLKLNWENPDIMSELLFQNNIIMFKNGDDLRQDMLTLQIIRIMENIWQNQGLDLRMLPYGCLSIGDCVGLIEWVRNSHTIMQIQCNSHTLHQWLKDKNKGEIYDAAIDLFTRSCAGYCVATFILGIGDRHNSNIMVKDDGQLVHIDFGHFLDHKKKKFGYKRERVPFVLTQDFLIVISKGAQECTKTREFERFQEMCYKAYLAIRQHANLFINLFSMMLGSGMPELQSFDDIAYIRKTLALDKTEQEALEYFMKQMNDAHHGGWTT 1053
                                    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  ||   330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500|      533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803       813       823       833       843       853       873       883       893       903       913       923       933       943       953       963       973       983       993      1003      1013      1023      1033      1043      1053
                                                                                                                                                                                                                                                             229|                                                                       311|                                                                                                                                                                             500|                                                                                                                                                                                                                                                                                                                                               862|                                                                                                                                                                                    
                                                                                                                                                                                                                                                              237                                                                        324                                                                                                                                                                              524                                                                                                                                                                                                                                                                                                                                                873                                                                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:257
                                                                                                                                                                                                                                                                                                  
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhh.....eeeeee.....eeeeeee..eeeeeeeeee..eee........hhhhhhhhhhhhh...........ee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5ul1 B  327 SLQDAEWYWGDISREEVNEKLRDTADGTFLVRDASTKDYTLTLRKGGNNKLIKIFHRDGKYGFSDPLTFSSVVELINHYRNESLAQYNPDVKLLYPVSKYQQDKEDNIEAVGKKLHEYNTQFQEKSREYDRLYEEYTRTSQEIQMKRTAIEAFNETIKIFEEQCQTQERYSKEYIEKFKREGNEKEIQRIMHNYDKLKSRISEIIDSRRRLEEDLKKQAAEYREIDKRMNSIKPDLIQLRKTRDQYLMWLTQKGVRQ  591
                                   336       346       356      |369       379       389       399       409       421       431  ||   444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       
                                                              363|                                                418|          434|                                                                                                                                                         
                                                               367                                                 421           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 5UL1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5UL1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5UL1)

(-) Gene Ontology  (109, 132)

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  P85A_HUMAN | P27986
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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 5uk8 5ukj 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 5uk8 5ukj

(-) Related Entries Specified in the PDB File

5uk8 5ukj