PDB entry 5vp1

View 5vp1 on RCSB PDB site
Description: Discovery of Clinical Candidate N-{(1S)-1-[3-Fluoro-4-(trifluoromethoxy)phenyl]-2-methoxyethyl}-7-methoxy-2-oxo-2,3-dihydropyrido[2,3-b]pyrazine-4(1H)-carboxamide (TAK-915), A Highly Potent, Selective, and Brain-Penetrating Phosphodiesterase 2A Inhibitor for the Treatment of Cognitive Disorders
Class: Hydrolase/Hydrolase Inhibitor
Keywords: Inhibitor, Phosphodiesterase, Brain-Pentrating, Cognitive Disorders, Hydrolase-Hydrolase Inhibitor complex
Deposited on 2017-05-03, released 2017-12-27
The last revision prior to the SCOPe 2.07 freeze date was dated 2017-12-27, with a file datestamp of 2017-12-22.
Experiment type: XRAY
Resolution: 1.86 Å
R-factor: N/A
AEROSPACI score: 0.36 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: cGMP-dependent 3',5'-cyclic phosphodiesterase
    Species: Homo sapiens [TaxId:9606]
    Gene: PDE2A
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d5vp1a_
  • Chain 'B':
    Compound: cGMP-dependent 3',5'-cyclic phosphodiesterase
    Species: Homo sapiens [TaxId:9606]
    Gene: PDE2A
    Database cross-references and differences (RAF-indexed):
    • Uniprot O00408 (3-End)
      • expression tag (0-2)
    Domains in SCOPe 2.07: d5vp1b1, d5vp1b2
  • Chain 'C':
    Compound: cGMP-dependent 3',5'-cyclic phosphodiesterase
    Species: Homo sapiens [TaxId:9606]
    Gene: PDE2A
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d5vp1c_
  • Heterogens: ZN, MG, 9GA, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >5vp1A (A:)
    ghasddeytkllhdgiqpvaaidsnfasftytprslpeddtsmailsmlqdmnfinnyki
    dcptlarfclmvkkgyrdppyhnwmhafsvshfcyllyknleltnyledieifalfiscm
    chdldhrgtnnsfqvasksvlaalyssegsvmerhhfaqaiailnthgcnifdhfsrkdy
    qrmldlmrdiilatdlahhlrifkdlqkmaevgydrnnkqhhrlllcllmtscdlsdqtk
    gwkttrkiaeliykeffsqgdlekamgnrpmemmdrekayipelqisfmehiampiykll
    qdlfpkaaelyervasnrehwtkvshkftirglpsnnsldfldee
    

    Sequence, based on observed residues (ATOM records): (download)
    >5vp1A (A:)
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    larfclmvkkgyrdppyhnwmhafsvshfcyllyknleltnyledieifalfiscmchdl
    dhrgtnnsfqvasksvlaalyssegsvmerhhfaqaiailnthgcnifdhfsrkdyqrml
    dlmrdiilatdlahhlrifkdlqkmaevgydrnnkqhhrlllcllmtscdlsdqtkgwkt
    trkiaeliykeffsqgdlekamgnrpmemmdrekayipelqisfmehiampiykllqdlf
    pkaaelyervasnrehwtkvshkftirglpsnnsldfl
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >5vp1B (B:)
    ghasddeytkllhdgiqpvaaidsnfasftytprslpeddtsmailsmlqdmnfinnyki
    dcptlarfclmvkkgyrdppyhnwmhafsvshfcyllyknleltnyledieifalfiscm
    chdldhrgtnnsfqvasksvlaalyssegsvmerhhfaqaiailnthgcnifdhfsrkdy
    qrmldlmrdiilatdlahhlrifkdlqkmaevgydrnnkqhhrlllcllmtscdlsdqtk
    gwkttrkiaeliykeffsqgdlekamgnrpmemmdrekayipelqisfmehiampiykll
    qdlfpkaaelyervasnrehwtkvshkftirglpsnnsldfldee
    

    Sequence, based on observed residues (ATOM records): (download)
    >5vp1B (B:)
    ghasddeytkllhdgiqpvaaidsnfasftytprslpeddtsmailsmlqdmnfinnyki
    dcptlarfclmvkkgyrdppyhnwmhafsvshfcyllyknleltnyledieifalfiscm
    chdldhrgtnnsfqvasksvlaalyssegsvmerhhfaqaiailnthgcnifdhfsrkdy
    qrmldlmrdiilatdlahhlrifkdlqkmaevgydrnnkqhhrlllcllmtscdlsdqtk
    gwkttrkiaeliykeffsqgdlekamgnrpmemmdrekayipelqisfmehiampiykll
    qdlfpkaaelyervasnrehwtkvshkftirglpsnnsldfl
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >5vp1C (C:)
    ghasddeytkllhdgiqpvaaidsnfasftytprslpeddtsmailsmlqdmnfinnyki
    dcptlarfclmvkkgyrdppyhnwmhafsvshfcyllyknleltnyledieifalfiscm
    chdldhrgtnnsfqvasksvlaalyssegsvmerhhfaqaiailnthgcnifdhfsrkdy
    qrmldlmrdiilatdlahhlrifkdlqkmaevgydrnnkqhhrlllcllmtscdlsdqtk
    gwkttrkiaeliykeffsqgdlekamgnrpmemmdrekayipelqisfmehiampiykll
    qdlfpkaaelyervasnrehwtkvshkftirglpsnnsldfldee
    

    Sequence, based on observed residues (ATOM records): (download)
    >5vp1C (C:)
    iqpvaaidsnfasftytprslpeddtsmailsmlqdmnfinnykidcptlarfclmvkkg
    yrdppyhnwmhafsvshfcyllyknleltnyledieifalfiscmchdldhrgtnnsfqg
    svmerhhfaqaiailnthgcnifdhfsrkdyqrmldlmrdiilatdlahhlrifkdlqkm
    aevgydrnnkqhhrlllcllmtscdlsdqtkgwkttrkiaeliykeffsqgdlekamgnr
    pmemmdrekayipelqisfmehiampiykllqdlfpkaaelyervasnrehwtkvshkft
    irglpsnnsldfl