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 :  CRYSTAL STRUCTURE OF PLK1 IN COMPLEX WITH A NOVEL 5,6-DIHYDROIMIDAZOLO[1,5-F]PTERIDINE INHIBITOR.
 
Authors :  R. J. Skene, D. J. Hosfield
Date :  09 Sep 16  (Deposition) - 22 Feb 17  (Release) - 08 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Plk1 Inhibitor, Kinase, Structure-Based Drug Design, Antitumor Activity, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Kiryanov, S. Natala, B. Jones, C. Mcbride, V. Feher, B. Lam, Y. Liu, K. Honda, N. Uchiyama, T. Kawamoto, Y. Hikichi, L. Zhang, D. Hosfield, R. Skene, H. Zou, J. Stafford, X. Cao, T. Ichikawa
Structure-Based Design And Sar Development Of 5, 6-Dihydroimidazolo[1, 5-F]Pteridine Derivatives As Novel Polo-Like Kinase-1 Inhibitors.
Bioorg. Med. Chem. Lett. V. 27 1311 2017
PubMed-ID: 28169164  |  Reference-DOI: 10.1016/J.BMCL.2016.10.009

(-) Compounds

Molecule 1 - SERINE/THREONINE-PROTEIN KINASE PLK1
    Chains: A
    EC Number: 2.7.11.21
    Engineered: YES
    Expression System: UNIDENTIFIED BACULOVIRUS
    Expression System Taxid: 10469
    Fragment: UNP RESIDUES 13-345
    Gene: PLK1, PLK
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: POLO-LIKE KINASE 1,PLK-1,SERINE/THREONINE-PROTEIN KINASE 13, STPK13

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
179D1Ligand/Ion4-{[(6R)-7-CYANO-5-CYCLOPENTYL-6-ETHYL-5,6-DIHYDROIMIDAZO[1,5-F]PTERIDIN-3-YL]AMINO}-3-METHOXY-N-(1-METHYLPIPERIDIN-4-YL)BENZAMIDE
2ZN1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:59 , LYS A:61 , CYS A:67 , GLU A:69 , VAL A:114 , GLU A:131 , LEU A:132 , CYS A:133 , ARG A:134 , ARG A:136 , PHE A:183 , ASP A:194 , HOH A:1112binding site for residue 79D A 1000
2AC2SOFTWAREHIS A:93 , CYS A:212 , CYS A:255 , LEU A:256 , HOH A:1188binding site for residue ZN A 1001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5TA6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5TA6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5TA6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5TA6)

(-) Exons   (0, 0)

(no "Exon" information available for 5TA6)

(-) 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:294
                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eee......eeeeeeeeeee..eeeeeeee.....eeeeeeee.hhh.hhhhhhhhhhhhhhhhh........eeeeee...eeeeeee.....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee..................hhhhhh.....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh........hhhhhhhhhhhh..hhhhh....hhhhhhhhhh.......hhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ta6 A  37 AKEIPEVLVDPRSRRRYVRGRFLGKGGFAKCFEISDADTKEVFAGKIVPKSLLLKPHQREKMSMEISIHRSLAHQHVVGFHGFFEDNDFVFVVLELCRRRSLLELHKRRKALTEPEARYYLRQIVLGCQYLHRNRVIHRDLKLGNLFLNEDLEVKIGDFGLATKVEYDGERKKVLCGTPNYIAPEVLSKKGHSFEVDVWSIGCIMYTLLVGKPPFETSCLKETYLRIKKNEYSIPKHINPVAASLIQKMLQTDPTARPTINELLNDEFFTSGYIPARLPITCLTIPPRFSIAPS 330
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326
   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 5TA6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5TA6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5TA6)

(-) Gene Ontology  (73, 73)

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
    79D  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5ta6)
 

(-) 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
  5ta6
    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
  PLK1_HUMAN | P53350
    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)
  2.7.11.21
    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
  PLK1_HUMAN | P53350
    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
        PLK1_HUMAN | P53350: 1q4k 1q4o 1umw 2ogq 2ojx 2ou7 2owb 2rku 2v5q 2yac 3bzi 3c5l 3fc2 3fvh 3hih 3hik 3kb7 3p2w 3p2z 3p34 3p35 3p36 3p37 3q1i 3rq7 3thb 4a4l 4a4o 4dfw 4e67 4e9c 4e9d 4h5x 4h71 4hab 4hco 4hy2 4j52 4j53 4lkl 4lkm 4o56 4o6w 4o9w 4rcp 4whh 4whk 4whl 4x9r 4x9v 4x9w 5j19 5ta8

(-) Related Entries Specified in the PDB File

5ta8