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Crystal structure of the PDE9A catalytic domain in complex with inhibitor 28
Biology and Chemistry Report
4GH6
  •   Structure Details   Hide

    Structure Keywords

    Keywords HYDROLASE/Hydrolase Inhibitor
    Text PDE9A,, HYDROLASE-Hydrolase Inhibitor complex

    Polymeric Molecules

    Chain A,B
    Description High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A 
    Fragment UNP residues 241-566 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 38546.8 
    Source Method genetically manipulated  

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    LUO  N-(4-methoxyphenyl)-N~2~-[1-(2-methylphenyl)-4-oxo-4,5-dihydro-1H-pyrazolo[3,4-d]pyrimidin-6-yl]-L-alaninamide  C22 H22 N6 O3   418.45  View 
    MG  MAGNESIUM ION  Mg   24.31  View 
    ZN  ZINC ION  Zn   65.41  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,B PDE9A_HUMAN B2RBI5     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    A B  3.1.4.35      
     
  •   Gene Details   Hide

    Genetic Source

    Chain A,B
    Common Name Human
    Scientific Name Homo sapiens  
    Gene pde9a
    Host Scientific Name Escherichia coli  
    Host Strain Bl21(codonplus)
    Host Vector Type Plasmid
    Host Plasmid Name pET15b


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    21 21q22.3 5152     phosphodiesterase 9A PDE9A    

    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
    rs183475207 LS-SNP   dbSNP   A 194 E - > Q Helix 57% (Exposed) 21 44174124
    rs188819062 LS-SNP   dbSNP   A 203 V - > I 3/10 Helix 0% (Buried) 21 44174151
    rs146382324 LS-SNP   dbSNP   A 212 L - > V Helix 2% (Buried) 21 44179112
    rs143538403 LS-SNP   dbSNP   A 223 G - > R Turn 1% (Buried) 21 44179145
    rs144720521 LS-SNP   dbSNP   A 258 F - > L Helix 0% (Buried) 21 44180494
    rs141486724 LS-SNP   dbSNP   A 288 A - > V Helix 0% (Buried) 21 44180975
    rs139964261 LS-SNP   dbSNP   A 295 D - > Y Turn 23% (Intermediate) 21 44180995
    rs140134669 LS-SNP   dbSNP   A 327 A - > T Helix 25% (Intermediate) 21 44182266
    rs145560514 LS-SNP   dbSNP   A 332 I - > N Helix 4% (Buried) 21 44182282
    rs140836666 LS-SNP   dbSNP   A 334 A - > T Turn 67% (Exposed) 21 44182287
    rs201884723 LS-SNP   dbSNP   A 335 E - > K Bend 49% (Exposed) 21 44182290
    rs201281940 LS-SNP   dbSNP   A 355 G - > V Helix 15% (Intermediate) 21 44185492
    rs191942684 LS-SNP   dbSNP   A 369 A - > G Helix 58% (Exposed) 21 44185534
    rs146611085 LS-SNP   dbSNP   A 373 D - > N Helix 60% (Exposed) 21 44185545
    rs151254797 LS-SNP   dbSNP   A 391 T - > I Helix 32% (Intermediate) 21 44185600
    rs13047465 LS-SNP   dbSNP   A 400 C - > Y Helix 1% (Buried) 21 44188320
    rs149967454 LS-SNP   dbSNP   A 410 M - > V Helix 30% (Intermediate) 21 44188349
    rs144998592 LS-SNP   dbSNP   A 419 C - > S Helix 18% (Intermediate) 21 44188377
    rs140957640 LS-SNP   dbSNP   A 432 K - > R Helix 42% (Exposed) 21 44189150
    rs201490586 LS-SNP   dbSNP   A 433 S - > A Turn 80% (Exposed) 21 44189152
    rs200824316 LS-SNP   dbSNP   A 454 I - > T Helix 9% (Buried) 21 44189216
    rs199846131 LS-SNP   dbSNP   A 467 T - > R Helix 8% (Buried) 21 44189255
    rs143437759 LS-SNP   dbSNP   A 479 M - > V Helix 0% (Buried) 21 44190837
    rs141574765 LS-SNP   dbSNP   A 492 E - > D Helix 62% (Exposed) 21 44190878
    rs150892798 LS-SNP   dbSNP   A 495 R - > Q Helix 63% (Exposed) 21 44190886
    rs201811895 LS-SNP   dbSNP   A 499 A - > T Helix 48% (Exposed) 21 44190897
    rs75225742 LS-SNP   dbSNP   A 500 M - > R Helix 57% (Exposed) 21 44190901