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Crystal Structure of PDE10A with a biaryl ether inhibitor ((1-(3-(4-((1H-benzo[d]imidazol-2-yl)amino)phenoxy)pyridin-2-yl)piperidin-4-yl)methanol)
Biology and Chemistry Report
  •   Structure Details   Hide

    Structure Keywords

    Keywords hydrolase/hydrolase inhibitor
    Text PDE10A, inhibitors, phosphodiesterase 10A, biaryl ethers, hydrolase-hydrolase inhibitor complex

    Polymeric Molecules

    Chain A,B
    Description cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A 
    Fragment human PDE10a, residues 442-779 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 36857.7 
    Source Method genetically manipulated  

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    15J  (1-{3-[4-(1H-benzimidazol-2-ylamino)phenoxy]pyridin-2-yl}piperidin-4-yl)methanol  C24 H25 N5 O2   415.49  View 
    SO4  SULFATE ION  O4 S   96.06  View 
    ZN  ZINC ION  Zn   65.41  View 
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,B PDE10_HUMAN Q9Y233     

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    A B      
    A B      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A,B
    GO ID   Ontology GO Term Definition
    7165   Signal Transduction  The Cellular Process in Which a Signal Is Conveyed to Trigger a Change in the Activity or State of a Cell. Signal Transduction Begins with Reception of a Signal (e.g. a Ligand Binding to a Receptor or Receptor Activation by a Stimulus Such As Light) or For Signal Transduction in the Absence of Ligand Signal Withdrawal or the Activity of a Constitutively Active Receptor. Signal Transduction Ends with Regulation of a Downstream Cellular Process E.g. Regulation of Transcription or Regulation of a Metabolic Process. Signal Transduction Covers Signaling From Receptors Located On the Surface of the Cell and Signaling Via Molecules Located Within the Cell. For Signaling Between Cells Signal Transduction Is Restricted to Events At and Within the Receiving Cell. 
    4114   3' 5' Cyclic Nucleotide Phosphodiesterase Activity  Catalysis of the Reaction: Nucleoside 3' 5' Cyclic Phosphate + H2o = Nucleoside 5' Phosphate. 
    8081   Phosphoric Diester Hydrolase Activity  Catalysis of the Hydrolysis of a Phosphodiester to Give a Phosphomonoester and a Free Hydroxyl Group. 

    Protein Analyses

    Measured Binding Affinities   

  •   Gene Details   Hide

    Genetic Source

    Chain A,B
    Common Name Human
    Scientific Name Homo sapiens  
    Gene pde10a
    Host Scientific Name Escherichia coli  

    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    6 6q26 10846     phosphodiesterase 10A PDE10A    

    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
    rs113840141 LS-SNP   dbSNP   A 451 Q - > R Coil 78% (Exposed) 6 165809845
    rs61733392 LS-SNP   dbSNP   A 477 P - > A Helix 17% (Intermediate) 6 165808716
    rs140135628 LS-SNP   dbSNP   A 484 V - > I Helix 1% (Buried) 6 165808695
    rs79937339 LS-SNP   dbSNP   A 486 R - > Q Helix 52% (Exposed) 6 165808688
    rs200615367 LS-SNP   dbSNP   A 600 I - > V Turn 4% (Buried) 6 165792840
    rs113894012 LS-SNP   dbSNP   A 603 T - > A Turn 86% (Exposed) 6 165792831
    rs138994439 LS-SNP   dbSNP   A 654 R - > H Helix 34% (Intermediate) 6 165756986
    rs117826255 LS-SNP   dbSNP   A 674 V - > I Helix 24% (Intermediate) 6 165756927
    rs148138380 LS-SNP   dbSNP   A 701 I - > M Coil 61% (Exposed) 6 165752812
    rs2224252 LS-SNP   dbSNP   A 706 R - > K 3/10 Helix 32% (Intermediate) 6 165752798
    rs2860112 LS-SNP   dbSNP   A 707 D - > N 3/10 Helix 75% (Exposed) 6 165752796
    rs199519823 LS-SNP   dbSNP   A 755 V - > A Helix 39% (Exposed) 6 165746590
    rs145722515 LS-SNP   dbSNP   A 757 R - > Q Turn 64% (Exposed) 6 165746584