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(-) Description

Title :  SCAFFOLD FOCUSED VIRTUAL SCREENING: PROSPECTIVE APPLICATION TO THE DISCOVERY OF TTK INHIBITOR
 
Authors :  S. R. Langdon, I. M. Westwood, R. L. M. Van Montfort, N. Brown, J. Blagg
Date :  09 Apr 13  (Deposition) - 22 May 13  (Release) - 05 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.85
Chains :  Asym./Biol. Unit :  A
Keywords :  Transferase, Mitosis (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. R. Langdon, I. M. Westwood, R. L. M. Van Montfort, N. Brown, J. Blagg
Scaffold-Focused Virtual Screening: Prospective Application To The Discovery Of Ttk Inhibitors.
J. Chem. Inf. Model V. 53 1100 2013
PubMed-ID: 23672464  |  Reference-DOI: 10.1021/CI400100C

(-) Compounds

Molecule 1 - DUAL SPECIFICITY PROTEIN KINASE TTK
    ChainsA
    EC Number2.7.12.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VariantAI
    FragmentKINASE DOMAIN, RESIDUES 518-807
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPHOSPHOTYROSINE PICKED THREONINE-PROTEIN KINASE, PYT, MONOPOLAR SPINDLE KINASE 1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
17PE2Ligand/Ion2-(2-(2-(2-(2-(2-ETHOXYETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHANOL
2EDO1Ligand/Ion1,2-ETHANEDIOL
3Z0B1Ligand/IonTHIENO[2,3-C][2,6]NAPHTHYRIDINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:537 , VAL A:539 , LYS A:553 , VAL A:555 , TYR A:568 , GLU A:571 , MET A:600 , ILE A:663 , Z0B A:1797BINDING SITE FOR RESIDUE 7PE A1795
2AC2SOFTWARETRP A:622 , LYS A:625 , SER A:626 , LYS A:629 , VAL A:791 , GLN A:792BINDING SITE FOR RESIDUE 7PE A1796
3AC3SOFTWAREILE A:531 , ALA A:551 , ILE A:586 , GLU A:603 , GLY A:605 , LEU A:654 , 7PE A:1795 , EDO A:1798BINDING SITE FOR RESIDUE Z0B A1797
4AC4SOFTWARELYS A:529 , GLN A:541 , ASN A:606 , Z0B A:1797BINDING SITE FOR RESIDUE EDO A1798

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_037142D758NTTK_HUMANPolymorphism2230512AD758N

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.TTK_HUMAN531-553  1A:531-553
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.TTK_HUMAN643-655  1A:643-655

(-) Exons   (0, 0)

(no "Exon" information available for 4BHZ)

(-) 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:251
 aligned with TTK_HUMAN | P33981 from UniProtKB/Swiss-Prot  Length:857

    Alignment length:279
                                   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         
            TTK_HUMAN   516 ECISVKGRIYSILKQIGSGGSSKVFQVLNEKKQIYAIKYVNLEEADNQTLDSYRNEIAYLNKLQQHSDKIIRLYDYEITDQYIYMVMECGNIDLNSWLKKKKSIDPWERKSYWKNMLEAVHTIHQHGIVHSDLKPANFLIVDGMLKLIDFGIANQMQPDTTSVVKDSQVGTVNYMPPEAIKDMSSSRENGKSKSKISPKSDVWSLGCILYYMTYGKTPFQQIINQISKLHAIIDPNHEIEFPDIPEKDLQDVLKCCLKRDPKQRISIPELLAHPYVQIQ 794
               SCOP domains d4bhza_ A: automa   ted matches                                                                                                                                                                                                                                                         SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eeeeeeee..---.eeeeeeee....eeeeeeee....hhhhhhhhhhhhhhhhhhh........eeeeee...eeeeee....eehhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee....eee........------------........hhhhhhh-------------.hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhh...........hhhhhhhhhhhh..hhhhh.hhhhhh.hhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------N------------------------------------ SAPs(SNPs)
                    PROSITE ---------------PROTEIN_KINASE_ATP     -----------------------------------------------------------------------------------------PROTEIN_KINAS------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bhz A 516 QSMSVKGRIYSILKQIG---SSKVFQVLNEKKQIYAIKYVNLEEADNQTLDSYRNEIAYLNKLQQHSDKIIRLYDYEITDQYIYMVMECGNIDLNSWLKKKKSIDPWERKSYWKNMLEAVHTIHQHGIVHSDLKPANFLIVDGMLKLIDFGIANQ------------QVGTVNYMPPEAIKD-------------ISPKSDVWSLGCILYYMTYGKTPFQQIINQISKLHAIIDPNHEIEFPDIPEKDLQDVLKCCLKRDPKQRISIPELLAHPYVQIQ 794
                                   525      |  -|      545       555       565       575       585       595       605       615       625       635       645       655       665    |    -       685       695 |       -     | 715       725       735       745       755       765       775       785         
                                          532 536                                                                                                                                   670          683           697           711                                                                                   

   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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (TTK_HUMAN | P33981)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0004672    protein kinase activity    Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
    GO:0004674    protein serine/threonine kinase activity    Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate.
    GO:0004712    protein serine/threonine/tyrosine kinase activity    Catalysis of the reactions: ATP + a protein serine = ADP + protein serine phosphate; ATP + a protein threonine = ADP + protein threonine phosphate; and ATP + a protein tyrosine = ADP + protein tyrosine phosphate.
    GO:0004713    protein tyrosine kinase activity    Catalysis of the reaction: ATP + a protein tyrosine = ADP + protein tyrosine phosphate.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0051304    chromosome separation    The cell cycle process in which paired chromosomes are detached from each other. Chromosome separation begins with the release of cohesin complexes from chromosomes; in budding yeast, this includes the cleavage of cohesin complexes along the chromosome arms, followed by the separation of the centromeric regions. Chromosome separation also includes formation of chromatid axes mediated by condensins, and ends with the disentangling of inter-sister catenation catalyzed by topoisomerase II (topo II).
    GO:0007093    mitotic cell cycle checkpoint    A cell cycle checkpoint that ensures accurate chromosome replication and segregation by preventing progression through a mitotic cell cycle until conditions are suitable for the cell to proceed to the next stage.
    GO:0007094    mitotic spindle assembly checkpoint    A cell cycle checkpoint that delays the metaphase/anaphase transition of a mitotic nuclear division until the spindle is correctly assembled and chromosomes are attached to the spindle.
    GO:0007052    mitotic spindle organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the microtubule spindle during a mitotic cell cycle.
    GO:0018108    peptidyl-tyrosine phosphorylation    The phosphorylation of peptidyl-tyrosine to form peptidyl-O4'-phospho-L-tyrosine.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    GO:0010862    positive regulation of pathway-restricted SMAD protein phosphorylation    Any process that increases the rate, frequency or extent of pathway-restricted SMAD protein phosphorylation. Pathway-restricted SMAD proteins and common-partner SMAD proteins are involved in the transforming growth factor beta receptor signaling pathways.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0007051    spindle organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the spindle, the array of microtubules and associated molecules that forms between opposite poles of a eukaryotic cell during DNA segregation and serves to move the duplicated chromosomes apart.
cellular component
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005819    spindle    The array of microtubules and associated molecules that forms between opposite poles of a eukaryotic cell during mitosis or meiosis and serves to move the duplicated chromosomes apart.

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 Related Entries

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

UniProtKB/Swiss-Prot
        TTK_HUMAN | P339812x9e 2zmc 2zmd 3cek 3dbq 3gfw 3h9f 3hmn 3hmo 3hmp 3vqu 3w1f 3wyx 3wyy 3wzj 3wzk 4b94 4bi0 4bi1 4bi2 4c4e 4c4f 4c4g 4c4h 4c4i 4c4j 4cv8 4cv9 4cva 4d2s 4h7x 4h7y 4js8 4jt3 4o6l 4zeg 5ap0 5ap1 5ap2 5ap3 5ap4 5ap5 5ap6 5ap7 5eh0 5ehl 5eho 5ehy 5ei2 5ei6 5ei8 5ljj 5n7v 5n84 5n87 5n93 5n9s 5na0 5nad

(-) Related Entries Specified in the PDB File

4bi0 SCAFFOLD FOCUSED VIRTUAL SCREENING: PROSPECTIVE APPLICATION TO THE DISCOVERY OF TTK INHIBITOR
4bi1 SCAFFOLD FOCUSED VIRTUAL SCREENING: PROSPECTIVE APPLICATION TO THE DISCOVERY OF TTK INHIBITOR
4bi2 SCAFFOLD FOCUSED VIRTUAL SCREENING: PROSPECTIVE APPLICATION TO THE DISCOVERY OF TTK INHIBITOR