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Crystal structure of Human Phosphodiesterase 5 complexed with Vardenafil(Levitra)
Biology and Chemistry Report
1UHO
  •   Structure Details   Hide

    Structure Keywords

    Keywords hydrolase
    Text PDE5 inhibitor complex, hydrolase

    Polymeric Molecules

    Chain A
    Description cGMP-specific 3',5'-cyclic phosphodiesterase 
    Fragment catalytic domain 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 37530.6 
    Source Method genetically manipulated  
    Entity Name PDE5, Phosphodiesterase 5 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    MG  MAGNESIUM ION  Mg   24.31  View 
    VDN  2-{2-ETHOXY-5-[(4-ETHYLPIPERAZIN-1-YL)SULFONYL]PHENYL}-5-METHYL-7-PROPYLIMIDAZO[5,1-F][1,2,4]TRIAZIN-4(1H)-ONE  C23 H32 N6 O4 S   488.60  View 
    ZN  ZINC ION  Zn   65.41  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A PDE5A_HUMAN A0AV69     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    3.1.4.35      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A
    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
    Common Name Human
    Scientific Name Homo sapiens  
    Genus Homo
    Host Scientific Name Escherichia coli  
    Host Genus Escherichia
    Host Vector Type Plasmid
    Host Plasmid Name pET21b


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    4 4q27 8654     phosphodiesterase 5A, cGMP-specific PDE5A    

    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
    rs201567342 LS-SNP   dbSNP   A 539 E - > K Helix 56% (Exposed) 4 120460132
    rs142017762 LS-SNP   dbSNP   A 544 A - > V Helix 24% (Intermediate) 4 120460116
    rs201992682 LS-SNP   dbSNP   A 545 A - > V Helix 79% (Exposed) 4 120446849
    rs146620333 LS-SNP   dbSNP   A 558 D - > Y Bend 36% (Exposed) 4 120446811
    rs199919242 LS-SNP   dbSNP   A 563 D - > Y Coil 4% (Buried) 4 120446796
    rs202121251 LS-SNP   dbSNP   A 563 D - > E Coil 4% (Buried) 4 120446794
    rs182361575 LS-SNP   dbSNP   A 577 R - > W Helix 16% (Intermediate) 4 120446754
    rs201137519 LS-SNP   dbSNP   A 587 N - > K Helix 50% (Exposed) 4 120446722
    rs150334535 LS-SNP   dbSNP   A 594 V - > F Helix 19% (Intermediate) 4 120442215
    rs74858495 LS-SNP   dbSNP   A 607 R - > L Coil 33% (Intermediate) 4 120442175
    rs140281959 LS-SNP   dbSNP   A 608 K - > E Turn 77% (Exposed) 4 120442173
    rs200506990 LS-SNP   dbSNP   A 617 H - > R Helix 6% (Buried) 4 120442145 ZN
    rs200867498 LS-SNP   dbSNP   A 618 A - > G Helix 0% (Buried) 4 120442142
    rs199541416 LS-SNP   dbSNP   A 622 A - > S Helix 0% (Buried) 4 120442131
    rs199872206 LS-SNP   dbSNP   A 625 M - > T Helix 0% (Buried) 4 120442121
    rs116396619 LS-SNP   dbSNP   A 641 L - > P Helix 16% (Intermediate) 4 120440278
    rs201618319 LS-SNP   dbSNP   A 648 I - > T Helix 0% (Buried) 4 120440257
    rs200619248 LS-SNP   dbSNP   A 654 D - > N Turn 6% (Buried) 4 120440240 ZN,MG
    rs200210551 LS-SNP   dbSNP   A 658 R - > H Coil 51% (Exposed) 4 120440227
    rs200562028 LS-SNP   dbSNP   A 661 N - > H Coil 14% (Intermediate) 4 120440219 VDN
    rs199811295 LS-SNP   dbSNP   A 680 I - > V Helix 72% (Exposed) 4 120432252
    rs201830023 LS-SNP   dbSNP   A 739 I - > T Helix 8% (Buried) 4 120427061
    rs139979143 LS-SNP   dbSNP   A 740 R - > K Helix 61% (Exposed) 4 120427058
    rs200968351 LS-SNP   dbSNP   A 774 I - > V Helix 14% (Intermediate) 4 120425702
    rs200040557 LS-SNP   dbSNP   A 775 Q - > H Helix 2% (Buried) 4 120425697 VDN
    rs114886951 LS-SNP   dbSNP   A 778 I - > T Helix 8% (Buried) 4 120423809
    rs201756535 LS-SNP   dbSNP   A 788 D - > Y Helix 43% (Exposed) 4 120423780
    rs199517948 LS-SNP   dbSNP   A 799 I - > V Coil 50% (Exposed) 4 120423747
    rs144726852 LS-SNP   dbSNP   A 799 I - > T Coil 50% (Exposed) 4 120423746
    rs149385790 LS-SNP   dbSNP   A 803 D - > A Turn 56% (Exposed) 4 120422407
    rs150693234 LS-SNP   dbSNP   A 814 P - > Q Helix 10% (Intermediate) 4 120422374
    rs202047445 LS-SNP   dbSNP   A 821 I - > T Helix 0% (Buried) 4 120422353
    rs150671601 LS-SNP   dbSNP   A 821 I - > M Helix 0% (Buried) 4 120422352
    rs200768019 LS-SNP   dbSNP   A 828 L - > M Helix 1% (Buried) 4 120422333
    rs199573045 LS-SNP   dbSNP   A 830 E - > Q Helix 25% (Intermediate) 4 120422327
    rs144055854 LS-SNP   dbSNP   A 844 D - > G Helix 34% (Intermediate) 4 120419853