Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  PI3K ALPHA LIPID KINASE WITH ACTIVE SITE INHIBITOR
 
Authors :  P. A. Elkins
Date :  04 Mar 15  (Deposition) - 17 Jun 15  (Release) - 17 Jun 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  A
Keywords :  "Lipid Kinase", Inhibitor, Complex, Pi3K, Pi3K Alpha, Transferase- Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Yang, P. F. Medeiros, K. Raha, P. Elkins, K. E. Lind, R. Lehr, N. D. Adams, J. L. Burgess, S. J. Schmidt, S. D. Knight, K. R. Auger, M. D. Schaber, G. J. Franklin, Y. Ding, J. L. Delorey, P. A. Centrella, S. Mataruse, S. R. Skinner, M. A. Clark, J. W. Cuozzo, G. Evindar
Discovery Of A Potent Class Of Pi3K Alpha Inhibitors With Unique Binding Mode Via Encoded Library Technology (Elt).
Acs Med. Chem. Lett. V. 6 531 2015
PubMed-ID: 26005528  |  Reference-DOI: 10.1021/ACSMEDCHEMLETT.5B00025
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOSPHATIDYLINOSITOL 3-KINASE REGULATORY SUBUNIT ALPHA, PHOSPHATIDYLINOSITOL 4,5-BISPHOSPHATE 3-KINASE CATALYTIC SUBUNIT ALPHA ISOFORM FUSION PROTEIN
    ChainsA
    EC Number2.7.1.153, 2.7.11.1
    EngineeredYES
    Expression SystemUNIDENTIFIED BACULOVIRUS
    Expression System Taxid10469
    FragmentUNP P27986 RESIDUES 318-615, LINKER (GSPGISGGGGG), P42336 RESIDUES 2-1068
    GenePIK3R1, GRB1, PIK3CA
    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,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

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
14EL3Ligand/Ion3-(6-METHOXYPYRIDIN-3-YL)-5-[({4-[(5-METHYL-1,3,4-THIADIAZOL-2-YL)SULFAMOYL]PHENYL}AMINO)METHYL]BENZOICACID

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:1770 , MET A:1772 , SER A:1774 , LYS A:1776 , PRO A:1778 , LYS A:1802 , TYR A:1836 , ILE A:1848 , GLU A:1849 , VAL A:1851 , GLN A:1859 , SER A:1919 , MET A:1922 , ILE A:1932 , ASP A:1933binding site for residue 4EL A 2101
2AC2SOFTWARETRP A:1328 , VAL A:1329 , ASN A:1331 , HIS A:1495 , ARG A:1577 , 4EL A:2103binding site for residue 4EL A 2102
3AC3SOFTWAREHIS A:526 , LYS A:530 , TRP A:1328 , TYR A:1392 , PRO A:1394 , GLU A:1494 , HIS A:1495 , TRP A:1498 , ARG A:1577 , 4EL A:2102binding site for residue 4EL A 2103

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Asp A:394 -Pro A:395
2Ser A:1158 -Pro A:1159

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4YKN)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YKN)

(-) 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:1205
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhh.....eeeee..eeeeee..eeeeee............hhhhhhh.........ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........eeeeeee.....eeeeeee...hhhhhhhhhhhhhhhh.hhhhh.hhhhheeeee.....eeee.....hhhhh.....eeeee....hhhhhhhhhhhhhhhh..hhhhhh..hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh..........hhhhhh.....eeeeeeeee......eeeeeeeee...hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhheeeee.....ee....hhhhhhhhhhhhhhh...eeeeeehhhhhhh........hhhhh...hhhhh..eeeeeeeee.........eeeeeeeeee..ee....ee...ee....eeeeeeeeeee.hhh....eeeeeeeeee....eeeeeeeeeee..........eeeeee...........................eeeeee..........hhhhhhhhhhhhhhh..hhhhhhhhhhhhhh......hhhhhhhhhhh.hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh....hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh.ee.......ee...hhhhhee.......eeeeee....hhhhh..eeeeeeee...hhhhhhhhhhhhhhhhhhhhh..........eeeee..eeeee....eeehhhhhhhh..........hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh........eeee....eee....................hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4ykn A  331 AEWYWGDISREEVNEKLRDTADGTFLVRDYTLTLRKGGNNKLIKIFHYGFSDPLTVVELINHYRNKLDVKLLYPVYNTQFQEKSREYDRLYEEYTRTSQEIQMKRTAIEAFNETIKIFEEQCQTQERYSKEYIEKFKREGNEKEIQRIMHNYDKLKSRISEIIDSRRRLEEDLKKQAAEYREIDKRMNSIKPDLIQLRKTRDQYLWGIHLMPPRILVECLLPNGMIVTLECLREATLITIKHELFKEARKYPLHQLLQDESSYIFVSVTQEAEREEFFDETRRLCDLRLFQPFLKVIEPVGNREEKILNREIGFAIGMPVCEFDMVKDPEVQDFRRNILNVCKEAVDLRDLNSPHSRAMYVYPPNVESSPELPKHIYNKLDKGQIIVVIWVIVSPNNDKQKYTLKINHDCVPEQVIAEAIRKKTRSMLLSSEQLKLCVLEYQGKYILKVCGCDEYFLEKYPLSQYKYIRSCIMLGRMPNLMLMAKESLYSQLPMDCFTMPSYSRSTKSLWVINSALRIKILCATYVNVNIIDKIYVRTGIYHGGEPLCDNVNTQRVPCSNPRWNEWLNYDIYIPDLPRAARLCLSICSVKGAKEEHCPLAWGNINLFDYTDTLVSGKMALNLWPVPHGLEDLLNPIGVTGSNPNKETPCLELEFDWFSSVVKFPDMSVIEEHANWSVSRELRENDKEQLKAISTRDPLSEITEQEKDFLWSHRHYCVTIPEILPKLLLSVKWNSRDEVAQMYCLVKDWPPIKPEQAMELLDCNYPDPMVRGFAVRCLEKYLTDDKLSQYLIQLVQVLKYEQYLDNLLVRFLLKKALTNQRIGHFFFWHLKSEMHNKTVSQRFGLLLESYCRACGMYLKHLNRQVEAMEKLINLTDILKQEKKDETQKVQMKFLVEQMRRPDFMDALQGFLSPLNPAHQLGNLRLEECRIMSSAKRPLWLNWENPDIMSELLFQNNEIIFKNGDDLRQDMLTLQIIRIMENIWQNQGLDLRMLPYGCLSIGDCVGLIEVVRNSHTIMQIQCKGGLKGALQFNSHTLHQWLKDKNKGEIYDAAIDLFTRSCAGYCVATFILGIGDRHNSNIMVKDDGQLFHIDFGHFLDHKKKKERVPFVLTQDFLIVISKGAQECTKTREFERFQEMCYKAYLAIRQHANLFINLFSMMLGSGMPELQSFDDIAYIRKTLALDKTEQEALEYFMKQMNDAHHGGWT 2052
                                   340       350       368       378      |392    || 405    || 423    || 456       466       476       486       496       506       516       526       536       546       556       566       576   || 1015      1025      1035      1045      1055      1065      1075      1085      1095      1105      1115      1125      1135      1145      1155      1165      1175      1185      1195      1205      1215      1225      1235      1245      1255      1265      1275      1285      1295      1305   || 1328      1338      1348|     1360      1370      1380      1390      1400      1410||    1423      1433      1443      1453      1463      1473      1483      1493      1503|     1532      1542      1552      1562      1572      1582      1592      1602      1612      1622      1632      1642      1652      1662      1672      1682      1692      1702      1712      1722      1732      1742      1752      1762      1772      1782      1792      1802      1812      1822      1832      1842      1852      1862      1872      1882      1892      1902      1912      1922      1932      1942 ||   1957      1967      1977      1987      1997      2007      2017      2027      2037      2047     
                                                      359|              385|    397|      410|      428|                                                                                                                             580|                                                                                                                                                                                                                                                                                                       1309|                     1348|                                                        1411|                                                                                    1503|                                                                                                                                                                                                                                                                                                                                                                                                                                 1944|                                                                                                      
                                                       368               390     401       419       452                                                                                                                             1010                                                                                                                                                                                                                                                                                                        1323                      1351                                                         1415                                                                                     1523                                                                                                                                                                                                                                                                                                                                                                                                                                  1950                                                                                                      

   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 4YKN)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (109, 132)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    4EL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Asp A:394 - Pro A:395   [ RasMol ]  
    Ser A:1158 - Pro A:1159   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4ykn
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  P85A_HUMAN | P27986
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
  PK3CA_HUMAN | P42336
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.7.1.153
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
  2.7.11.1
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  P85A_HUMAN | P27986
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  PK3CA_HUMAN | P42336
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 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 4waf 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 4waf 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 4YKN)