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 PYRIMIDODIAZEPINONE INHIBITOR
 
Authors :  D. J. Hosfield, R. J. Skene
Date :  07 Feb 13  (Deposition) - 29 May 13  (Release) - 05 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Protein Serine/Threonine Kinase, Mitosis, Oncogenesis, Regulation Of Cell Cycle, Kinase Domain, Atp Binding, Nuclear, Transferase- Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Nie, V. Feher, S. Natala, C. Mcbride, A. Kiryanov, B. Jones, B. Lam, Y. Liu, S. Kaldor, J. Stafford, K. Hikami, N. Uchiyama, T. Kawamoto, Y. Hikichi, S. Matsumoto, N. Amano, L. Zhang, D. Hosfield, R. Skene, H. Zou, X. Cao, T. Ichikawa
Discovery Of Tak-960: An Orally Available Small Molecule Inhibitor Of Polo-Like Kinase 1 (Plk1).
Bioorg. Med. Chem. Lett. V. 23 3662 2013
PubMed-ID: 23664874  |  Reference-DOI: 10.1016/J.BMCL.2013.02.083

(-) Compounds

Molecule 1 - SERINE/THREONINE-PROTEIN KINASE PLK1
    Chains: A
    EC Number: 2.7.11.21
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Taxid: 7108
    Fragment: CATALYTIC DOMAIN (UNP RESIDUES 38-330)
    Gene: PLK1, PLK
    Mutation: YES
    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  (3, 3)

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
11J31Ligand/Ion4-{[(7R)-9-CYCLOPENTYL-7-ETHENYL-7-FLUORO-5-METHYL-6-OXO-6,7,8,9-TETRAHYDRO-5H-PYRIMIDO[4,5-B][1,4]DIAZEPIN-2-YL]AMINO}-3-METHOXY-N-(4-METHYLPIPERAZIN-1-YL)BENZAMIDE
2ACT1Ligand/IonACETATE ION
3ZN1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:57 , PHE A:58 , LEU A:59 , CYS A:67 , GLY A:81 , LYS A:82 , VAL A:114 , LEU A:130 , GLU A:131 , LEU A:132 , CYS A:133 , ARG A:134 , ARG A:136 , PHE A:183 , HOH A:505 , HOH A:561 , HOH A:575BINDING SITE FOR RESIDUE 1J3 A 400
2AC2SOFTWAREHIS A:93 , CYS A:212 , CYS A:255 , LEU A:256 , HOH A:578BINDING SITE FOR RESIDUE ZN A 401
3AC3SOFTWARELYS A:178 , LEU A:179 , GLY A:180 , ASN A:216 , TYR A:217 , HOH A:549 , HOH A:550BINDING SITE FOR RESIDUE ACT A 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4J52)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4J52)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4J52)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4J52)

(-) Exons   (0, 0)

(no "Exon" information available for 4J52)

(-) 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:293
                                                                                                                                                                                                                                                                                                                                     
               SCOP domains d4j52a_ A: automated matches                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee....eeeeeeeeee.....eeeeeee.....eeeeeeee.hhh.hhhhhhhhhhhhhhhh.........eeeeee...eeeeee......hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee..................hhhhhh.....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh........hhhhhhhhhhhh...........hhhhhhhhhh.......hhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j52 A  38 KEIPEVLVDPRSRRRYVRGRFLGKGGFAKCFEISDADTKEVFAGKIVPKSLLLKPHQREKMSMEISIHRSLAHQHVVGFHGFFEDNDFVFVVLELCRRRSLLELHKRRKALTEPEARYYLRQIVLGCQYLHRNRVIHRDLKLGNLFLNEDLEVKIGDFGLATKVEYDGERKKVLCGTPNYIAPEVLSKKGHSFEVDVWSIGCIMYTLLVGKPPFETSCLKETYLRIKKNEYSIPKHINPVAASLIQKMLQTDPTARPTINELLNDEFFTSGYIPARLPITCLTIPPRFSIAPS 330
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327
   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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4J52)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4J52)

(-) 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
    1J3  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ACT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4j52)
 

(-) 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
  4j52
    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 4j53 4lkl 4lkm 4o56 4o6w 4o9w 4rcp 4whh 4whk 4whl 4x9r 4x9v 4x9w 5j19 5ta6 5ta8

(-) Related Entries Specified in the PDB File

4j53