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Structure of CDK9 in complex with cyclin T and a 2-amino-4-heteroaryl- pyrimidine inhibitor
Biology and Chemistry Report
4BCJ
  •   Structure Details   Hide

    Structure Keywords

    Keywords TRANSFERASE/CELL CYCLE
    Text TRANSFERASE-CELL CYCLE COMPLEX, CDK-CYCLIN COMPLEX, TRANSCRIPTION-PROTEIN BINDING, STRUCTURE-BASED DRUG DESIGN

    Polymeric Molecules

    Chain A
    Description CYCLIN-DEPENDENT KINASE 9 
    Fragment RESIDUES 2-330 
    Nonstandard Linkage no 
    Nonstandard Monomers yes 
    Polymer Type polypeptide(L) 
    Formula Weight 38054.4 
    Source Method genetically manipulated  
    Entity Name C-2K, CELL DIVISION CYCLE 2-LIKE PROTEIN KINASE 4, CELL DIVISION PROTEIN KINASE 9, SERINE/THREONINE-PROTEIN KINASE PITALRE, TAT-ASSOCIATED KINASE COMPLEX CATALYTIC SUBUNIT 
    Chain B
    Description CYCLIN-T1 
    Fragment RESIDUES 2-259 
    Mutation YES 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 30119.6 
    Source Method genetically manipulated  
    Entity Name CYCT1, CYCLIN-T 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    T9N  2-[(3-hydroxyphenyl)amino]-4-[4-methyl-2-(methylamino)-1,3-thiazol-5-yl]pyrimidine-5-carbonitrile  C16 H14 N6 O S   338.39  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A CDK9_HUMAN P50750     
    B CCNT1_HUMAN A9XU13     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    2.7.11.22      
    2.7.11.23      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A
    GO ID   Ontology GO Term Definition
    6468   Protein Phosphorylation  The Process of Introducing a Phosphate Group On to a Protein. 
    4672   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. 
    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. 
    5524   ATP Binding  Interacting Selectively and Non Covalently with ATP Adenosine 5' Triphosphate a Universally Important Coenzyme and Enzyme Regulator. 
    16772   Transferase Activity Transferring Phosphorus Containing Groups  Catalysis of the Transfer of a Phosphorus Containing Group From One Compound (donor) to Another (acceptor). 
    Chain B
    GO ID   Ontology GO Term Definition
    79   Regulation of Cyclin Dependent Protein Serine/threonine Kinase Activity  Any Process That Modulates the Frequency Rate or Extent of Cyclin Dependent Protein Serine/threonine Kinase Activity. 
    6351   Transcription DNA Templated  The Cellular Synthesis of RNA On a Template of Dna. 
    6355   Regulation of Transcription DNA Templated  Any Process That Modulates the Frequency Rate or Extent of Cellular DNA Templated Transcription. 
    19901   Protein Kinase Binding  Interacting Selectively and Non Covalently with a Protein Kinase Any Enzyme That Catalyzes the Transfer of a Phosphate Group Usually From ATP to a Protein Substrate. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain B
    Common Name Human
    Scientific Name Homo sapiens  
    Host Common Name Fall Armyworm
    Host Scientific Name Spodoptera frugiperda  
    Host Strain Sf9
    Host Vector Type Baculovirus
    Host Plasmid Name PVL1392


    Chain A
    Common Name Human
    Scientific Name Homo sapiens  
    Host Common Name Fall Armyworm
    Host Scientific Name Spodoptera frugiperda  
    Host Strain Sf9
    Host Vector Type Baculovirus
    Host Plasmid Name PVL1392


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    9 9q34.1 1025     cyclin-dependent kinase 9 CDK9    
    12 12q13.11 904     cyclin T1 CCNT1    

    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
    rs146765767 LS-SNP   dbSNP   A 24 K - > R Beta Ladder 75% (Exposed) 9 130548498
    rs149950953 LS-SNP   dbSNP   A 58 G - > W Bend 6% (Buried) 9 130549059
    rs55640715 LS-SNP   dbSNP   A 59 F - > L Bend 5% (Buried) 9 130549799
    rs141709101 LS-SNP   dbSNP   A 87 T - > I Coil 36% (Intermediate) 9 130549882
    rs147073375 LS-SNP   dbSNP   A 108 H - > R Beta Ladder 39% (Exposed) 9 130550283 T9N
    rs148342102 LS-SNP   dbSNP   A 193 W - > R 3/10 Helix 39% (Exposed) 9 130550637
    rs141577691 LS-SNP   dbSNP   A 233 T - > M Bend 54% (Exposed) 9 130550916
    rs11554104 LS-SNP   dbSNP   A 239 A - > T Helix 11% (Intermediate) 9 130550933
    rs145977259 LS-SNP   dbSNP   A 298 L - > P Bend 1% (Buried) 9 130551596
    rs139856271 LS-SNP   dbSNP   A 304 I - > M Coil 14% (Intermediate) 9 130551615
    rs201190553 LS-SNP   dbSNP   B 36 S - > P Helix 41% (Exposed) 12 49110353
    rs147254693 LS-SNP   dbSNP   B 71 M - > T Turn 9% (Intermediate) 12 49108257
    rs201367358 LS-SNP   dbSNP   B 218 G - > R Bend 51% (Exposed) 12 49089836
    rs35965578 LS-SNP   dbSNP   B 227 A - > P Turn 85% (Exposed) 12 49089809
    rs11834413 LS-SNP   dbSNP   B 235 D - > N Helix 36% (Exposed) 12 49089785
    rs147384648 LS-SNP   dbSNP   B 241 F - > L Helix 0% (Buried) 12 49089596