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X-ray structure of human CDK6-Vcyclinwith the inhibitor aminopurvalanol
Biology and Chemistry Report
2F2C
  •   Structure Details   Hide

    Structure Keywords

    Keywords CELL CYCLE/TRANSFERASE
    Text Small molecule inhibitor bound between N-terminal and C-terminal domain of kinase, CELL CYCLE-TRANSFERASE COMPLEX

    Polymeric Molecules

    Chain A
    Description Cyclin homolog 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 28665.6 
    Source Method genetically manipulated  
    Entity Name V-cyclin 
    Chain B
    Description Cell division protein kinase 6 
    Fragment fragment 1-308 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 35066.6 
    Source Method genetically manipulated  
    Entity Name Serine/threonine-protein kinase PLSTIRE 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    AP9  (2S)-2-({6-[(3-AMINO-5-CHLOROPHENYL)AMINO]-9-ISOPROPYL-9H-PURIN-2-YL}AMINO)-3-METHYLBUTAN-1-OL  C19 H26 Cl N7 O   403.91  View 
    DMS  DIMETHYL SULFOXIDE  C2 H6 O S   78.13  View 
    SO4  SULFATE ION  O4 S   96.06  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A CGH2_SHV21 Q01043     
    B CDK6_HUMAN A4D1G0     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc Catalytic Site(s)
    2.7.11.22        
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A
    GO ID   Ontology GO Term Definition
    7049   Cell Cycle  The Progression of Biochemical and Morphological Phases and Events That Occur in a Cell During Successive Cell Replication or Nuclear Replication Events. Canonically the Cell Cycle Comprises the Replication and Segregation of Genetic Material Followed by the Division of the Cell But in Endocycles or Syncytial Cells Nuclear Replication or Nuclear Division May Not Be Followed by Cell Division. 
    16032   Viral Process  A Multi Organism Process in Which a Virus Is a Participant. the Other Participant Is the Host. Includes Infection of a Host Cell Replication of the Viral Genome and Assembly of Progeny Virus Particles. in Some Cases the Viral Genetic Material May Integrate Into the Host Genome and Only Subsequently Under Particular Circumstances 'complete' Its Life Cycle. 
    51301   Cell Division  The Process Resulting in the Physical Partitioning and Separation of a Cell Into Daughter Cells. 
    60153   Modulation by Virus of Host Cell Cycle  Any Viral Process That Modulates the Rate or Extent of Progression Through the Cell Cycle. 
    Chain B
    GO ID   Ontology GO Term Definition
    7049   Cell Cycle  The Progression of Biochemical and Morphological Phases and Events That Occur in a Cell During Successive Cell Replication or Nuclear Replication Events. Canonically the Cell Cycle Comprises the Replication and Segregation of Genetic Material Followed by the Division of the Cell But in Endocycles or Syncytial Cells Nuclear Replication or Nuclear Division May Not Be Followed by Cell Division. 
    16310   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. 
    30154   Cell Differentiation  The Process in Which Relatively Unspecialized Cells E.g. Embryonic or Regenerative Cells Acquire Specialized Structural And/or Functional Features That Characterize the Cells Tissues or Organs of the Mature Organism or Some Other Relatively Stable Phase of the Organism's Life History. Differentiation Includes the Processes Involved in Commitment of a Cell to a Specific Fate and Its Subsequent Development to the Mature State. 
    51301   Cell Division  The Process Resulting in the Physical Partitioning and Separation of a Cell Into Daughter Cells. 
    1726   Ruffle  Projection At the Leading Edge of a Crawling Cell; the Protrusions Are Supported by a Microfilament Meshwork. 
    5634   Nucleus  A Membrane Bounded Organelle of Eukaryotic Cells in Which Chromosomes Are Housed and Replicated. in Most Cells the Nucleus Contains All of the Cell's Chromosomes Except the Organellar Chromosomes and Is the Site of RNA Synthesis and Processing. in Some Species or in Specialized Cell Types RNA Metabolism or DNA Replication May Be Absent. 
    5737   Cytoplasm  All of the Contents of a Cell Excluding the Plasma Membrane and Nucleus But Including Other Subcellular Structures. 
    42995   Cell Projection  A Prolongation or Process Extending From a Cell E.g. a Flagellum or Axon. 
    166   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. 
    4674   Protein Serine/threonine Kinase Activity  Catalysis of the Reactions: ATP + Protein Serine = Adp + Protein Serine Phosphate and ATP + Protein Threonine = Adp + Protein Threonine Phosphate. 
    5515   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). 
    5524   ATP Binding  Interacting Selectively and Non Covalently with ATP Adenosine 5' Triphosphate a Universally Important Coenzyme and Enzyme Regulator. 
    16301   Kinase Activity  Catalysis of the Transfer of a Phosphate Group Usually From ATP to a Substrate Molecule. 
    16740   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. 
    30332   Cyclin Binding  Interacting Selectively and Non Covalently with Cyclins Proteins Whose Levels in a Cell Varies Markedly During the Cell Cycle Rising Steadily Until Mitosis Then Falling Abruptly to Zero. As Cyclins Reach a Threshold Level They Are Thought to Drive Cells Into G2 Phase and Thus to Mitosis. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain B
    Common Name Human
    Scientific Name Homo sapiens  
    Genus Homo
    Gene cdk6
    Host Common Name Fall Armyworm
    Host Scientific Name Spodoptera frugiperda  
    Host Genus Spodoptera


    Chain A
    Scientific Name Herpesvirus saimiri (strain 11)  
    Genus Rhadinovirus
    Species Saimiriine Herpesvirus 2
    Strain 11
    Gene 72, eclf2
    Host Common Name Fall Armyworm
    Host Scientific Name Spodoptera frugiperda  
    Host Genus Spodoptera


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    7 7q21-q22 1021     cyclin-dependent kinase 6 CDK6    

    Single Nucleotide Polymorphisms (from LS-SNP database)

    SNP ID LsSnp Link dbSNP Link Chain PDB position Amino acid changes Secondary structure Solvent Accessibility Chromosome Chromosome position Ligand
    rs200082521 LS-SNP   dbSNP   B 86 S - > P Coil 70% (Exposed) 7 92404123
    rs35654944 LS-SNP   dbSNP   B 110 D - > N Helix 52% (Exposed) 7 92404051