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 :  PI3 KINASE DELTA IN COMPLEX WITH N-[6-(5-METHANESULFONAMIDO-6-METHOXYPYRIDIN-3-YL)-1,3-DIHYDRO-2-BENZOFURAN-4-YL]-2-(MORPHOLIN-4-YL)ACETAMIDE
 
Authors :  P. Rowland
Date :  01 Jun 16  (Deposition) - 27 Jul 16  (Release) - 24 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.06
Chains :  Asym./Biol. Unit :  A
Keywords :  Pi3 Kinase Delta, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Amour, N. Barton, A. W. Cooper, G. Inglis, C. Jamieson, C. N. Luscombe, J. Morrell, S. Peace, D. Perez, P. Rowland, C. Tame, S. Uddin, G. Vitulli, N. Wellaway
Evolution Of A Novel, Orally Bioavailable Series Of Pi3K Delta Inhibitors From An Inhaled Lead For The Treatment Of Respiratory Disease.
J. Med. Chem. V. 59 7239 2016
PubMed-ID: 27429068  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.6B00799

(-) Compounds

Molecule 1 - PHOSPHATIDYLINOSITOL 4,5-BISPHOSPHATE 3-KINASE CATALYTIC SUBUNIT DELTA ISOFORM
    Chains: A
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Taxid: 7108
    Gene: PIK3CD
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
16PF1Ligand/IonN-[6-(5-METHANESULFONAMIDO-6-METHOXYPYRIDIN-3-YL)-1,3-DIHYDRO-2-BENZOFURAN-4-YL]-2-(MORPHOLIN-4-YL)ACETAMIDE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:752 , SER A:754 , PRO A:758 , LYS A:779 , LEU A:784 , ASP A:787 , ILE A:825 , GLU A:826 , VAL A:828 , ASN A:836 , MET A:900 , ASP A:911binding site for residue 6PF A 4000

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5L72)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5L72)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5L72)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5L72)

(-) Exons   (0, 0)

(no "Exon" information available for 5L72)

(-) 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:858
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh..hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh............eeeeeeee......eeeeee...hhhhhhhhhhhhhhhhhh.....hhh.eeeee.....ee....hhhhhhhhhhhhhh....eeeeeehhhhhhhhhh...hhhhh..eeeeeeeee.........eeeeeeeeee..ee....ee...ee.....eeeeeeeeeee........eeeeeeeee..eeeeeeeee..........eeeeee.ee....................eeeeee...........hhhhhhhhh........hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh..hhhhhhhhh...hhhhhhhhhhhhhh....hhhhhhhhhh....hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh.hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee..eeeeee.ee.hhhhee.......eeeeeee...eeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhhh..........eeeee..eeeee....eeehhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........eeee....eee................hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5l72 A  108 RVKKLINSQISLLIGKGLHEFDSLRDPEVNDFRTKMRQFCEEAAAHRQQLGWVEWLQYSFPLQLEPSARGNRALLVNVKFEGSEESFTFQVSTKDMPLALMACALRKKATVFRQPLVEQPEEYALQVNGRHEYLYGNYPLCHFQYICSCLHSGLTPHLTMVHSSSILAMRDEQSNSLWSLEQPFSIELIEGRKVNADERMKLVVQAGLFHGNEMLCKTVSSSEVNVCSEPVWKQRLEFDISVCDLPRMARLCFALYAVVDCPIAWANLMLFDYKDQLKTGERCLYMWPSVLLNPAGTVRGNPNTESAAALVIYLPEVAPHPVYFPALEKILELGRHGERGRITEEEQLQLREILERELYEHEKDLVWKMRHEVQEHFPEALARLLLVTKWNKHEDVAQMLYLLCSWPELPVLSALELLDFSFPDCYVGSFAIKSLRKLTDDELFQYLLQLVQVLKYESYLDCELTKFLLGRALANRKIGHFLFWHLRSEMHVPSVALRFGLIMEAYCRGSTHHMKVLMKQGEALSKLKALNDFVKVSSQKTTKPQTKEMMHMCMRQETYMEALSHLQSPLDPSTLLEEVCVEQCTFMDSKMKPLWIMYSSEEAGSAGNVGIIFKNGDDLRQDMLTLQMIQLMDVLWKQEGLDLRMTPYGCLPTGDRTGLIEVVLHSDTIANIQLNKSNMAATAAFNKDALLNWLKSKNPGEALDRAIEEFTLSCAGYCVATYVLGIGDRHSDNIMIRESGQLFHIDFGHFLGNERVPFILTYDFVHVIQQGKTNNSEKFERFRGYCERAYTILRRHGLLFLHLFALMRAAGLPELSCSKDIQYLKDSLALGKTEEEALKHFRVKFNEALRESWKTKVN 1032
                                   117       127       137       147       157       167       177|      196       206       216       226       236       246       256       266       276       286    || 319       329       339       349       359       369       379       389       415       425       435       445|      461       471       481       491       501       511     ||525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795       805       815       825       835       845       855       865       875       885       895       905       915  ||   934       944       954       964       974       984       994      1004      1014      1024        
                                                                                               177|                                                                                                     291|                                                                                398|                           445|                                                              517|                                                                                                                                                                                                                                                                                                                                                                                                         918|                                                                                                        
                                                                                                187                                                                                                      315                                                                                 415                            452                                                               522                                                                                                                                                                                                                                                                                                                                                                                                          928
   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 5L72)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5L72)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5L72)

(-) Gene Ontology  (29, 34)

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
    6PF  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5l72)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5l72
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  PK3CD_MOUSE | O35904
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  Q3UDT3_MOUSE | Q3UDT3
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  PK3CD_MOUSE | O35904
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  Q3UDT3_MOUSE | Q3UDT3
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        PK3CD_MOUSE | O35904: 2wxf 2wxg 2wxh 2wxi 2wxj 2wxk 2wxl 2wxm 2wxn 2wxo 2wxp 2wxq 2wxr 2x38 4ajw 4v0i 4xe0 5ae8 5ae9 5i4u 5i6u 5is5 5ncy 5ncz 5t27 5t28 5t2b 5t2d 5t2g 5t2i 5t2l 5t2m 5t7f 5t8i
        Q3UDT3_MOUSE | Q3UDT3: 2wxf 2wxg 2wxh 2wxi 2wxj 2wxk 2wxl 2wxm 2wxn 2wxo 2wxp 2wxq 2wxr 2x38 5ae8 5ae9 5is5

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5L72)