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Structure of CDK9 in complex with cyclin T and a 2-amino-4-heteroaryl- pyrimidine inhibitor
Biology and Chemistry Report
4BCF
  •   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 38068.5 
    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
    T6Q  2-[[3-(4-ethanoyl-1,4-diazepan-1-yl)phenyl]amino]-4-[4-methyl-2-(methylamino)-1,3-thiazol-5-yl]pyrimidine-5-carbonitrile  C23 H26 N8 O S   462.57  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      
     
  •   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 64% (Exposed) 9 130548498
    rs149950953 LS-SNP   dbSNP   A 58 G - > W Bend 4% (Buried) 9 130549059
    rs55640715 LS-SNP   dbSNP   A 59 F - > L Bend 7% (Buried) 9 130549799
    rs141709101 LS-SNP   dbSNP   A 87 T - > I Coil 33% (Intermediate) 9 130549882
    rs147073375 LS-SNP   dbSNP   A 108 H - > R Beta Ladder 41% (Exposed) 9 130550283 T6Q
    rs148342102 LS-SNP   dbSNP   A 193 W - > R 3/10 Helix 37% (Exposed) 9 130550637
    rs141577691 LS-SNP   dbSNP   A 233 T - > M Bend 60% (Exposed) 9 130550916
    rs11554104 LS-SNP   dbSNP   A 239 A - > T Helix 19% (Intermediate) 9 130550933
    rs145977259 LS-SNP   dbSNP   A 298 L - > P Bend 4% (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 35% (Intermediate) 12 49110353
    rs147254693 LS-SNP   dbSNP   B 71 M - > T Turn 8% (Buried) 12 49108257
    rs201367358 LS-SNP   dbSNP   B 218 G - > R Bend 55% (Exposed) 12 49089836
    rs35965578 LS-SNP   dbSNP   B 227 A - > P Turn 99% (Exposed) 12 49089809
    rs11834413 LS-SNP   dbSNP   B 235 D - > N Helix 37% (Exposed) 12 49089785
    rs147384648 LS-SNP   dbSNP   B 241 F - > L Helix 0% (Buried) 12 49089596