PDB entry 3v9b

View 3v9b on RCSB PDB site
Description: Crystal structure of the catalytic domain of PDE4D2 with (S)-N-(3-{1-[1-(3-Cyclopropylmethoxy-4-difluoromethoxyphenyl)-2-(1-oxypyridin-4-yl)-ethyl]-1H-pyrazl-3-yl}phenyl)acetamide
Class: hydrolase/hydrolase inhibitor
Keywords: hydrolase, 3',5'-Cyclic-AMP Phosphodiesterases, Cyclic nucleotide, phosphodiesterases, HYDROLASE-HYDROLASE INHIBITOR complex
Deposited on 2011-12-25, released 2012-01-18
The last revision prior to the SCOPe 2.04 freeze date was dated 2013-06-26, with a file datestamp of 2013-06-21.
Experiment type: XRAY
Resolution: 2.1 Å
R-factor: 0.206
AEROSPACI score: 0.42 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: cAMP-specific 3',5'-cyclic phosphodiesterase 4D
    Species: Homo sapiens [TaxId:9606]
    Gene: PDE4D
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.04: d3v9ba_
  • Chain 'B':
    Compound: cAMP-specific 3',5'-cyclic phosphodiesterase 4D
    Species: Homo sapiens [TaxId:9606]
    Gene: PDE4D
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.04: d3v9bb_
  • Chain 'C':
    Compound: cAMP-specific 3',5'-cyclic phosphodiesterase 4D
    Species: Homo sapiens [TaxId:9606]
    Gene: PDE4D
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.04: d3v9bc_
  • Chain 'D':
    Compound: cAMP-specific 3',5'-cyclic phosphodiesterase 4D
    Species: Homo sapiens [TaxId:9606]
    Gene: PDE4D
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.04: d3v9bd_
  • Heterogens: IHM, ZN, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >3v9bA (A:)
iprfgvkteqedvlakeledvnkwglhvfriaelsgnrpltvimhtifqerdllktfkip
vdtlitylmtledhyhadvayhnnihaadvvqsthvllstpaleavftdleilaaifasa
ihdvdhpgvsnqflintnselalmyndssvlenhhlavgfkllqeencdifqnltkkqrq
slrkmvidivlatdmskhmnlladlktmvetkkvtssgvllldnysdriqvlqnmvhcad
lsnptkplqlyrqwtdrimeeffrqgdrerergmeispmcdkhnasveksqvgfidyivh
plwetwadlvhpdaqdildtlednrewyqstipqspspapddpeegrqgqtekfqfeltl

    Sequence, based on observed residues (ATOM records): (download) 
    >3v9bA (A:)
fgvkteqedvlakeledvnkwglhvfriaelsgnrpltvimhtifqerdllktfkipvdt
litylmtledhyhadvayhnnihaadvvqsthvllstpaleavftdleilaaifasaihd
vdhpgvsnqflintnselalmyndssvlenhhlavgfkllqeencdifqnltkkqrqslr
kmvidivlatdmskhmnlladlktmvetkkvtssgvllldnysdriqvlqnmvhcadlsn
ptkplqlyrqwtdrimeeffrqgdrerergmeispmcdkhnasveksqvgfidyivhplw
etwadlvhpdaqdildtlednrewyqstipq

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >3v9bB (B:)
iprfgvkteqedvlakeledvnkwglhvfriaelsgnrpltvimhtifqerdllktfkip
vdtlitylmtledhyhadvayhnnihaadvvqsthvllstpaleavftdleilaaifasa
ihdvdhpgvsnqflintnselalmyndssvlenhhlavgfkllqeencdifqnltkkqrq
slrkmvidivlatdmskhmnlladlktmvetkkvtssgvllldnysdriqvlqnmvhcad
lsnptkplqlyrqwtdrimeeffrqgdrerergmeispmcdkhnasveksqvgfidyivh
plwetwadlvhpdaqdildtlednrewyqstipqspspapddpeegrqgqtekfqfeltl

    Sequence, based on observed residues (ATOM records): (download) 
    >3v9bB (B:)
teqedvlakeledvnkwglhvfriaelsgnrpltvimhtifqerdllktfkipvdtlity
lmtledhyhadvayhnnihaadvvqsthvllstpaleavftdleilaaifasaihdvdhp
gvsnqflintnselalmyndssvlenhhlavgfkllqeencdifqnltkkqrqslrkmvi
divlatdmskhmnlladlktmvetkkvtssgvllldnysdriqvlqnmvhcadlsnptkp
lqlyrqwtdrimeeffrqgdrerergmeispmcdkhnasveksqvgfidyivhplwetwa
dlvhpdaqdildtlednrewyqstipq

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >3v9bC (C:)
iprfgvkteqedvlakeledvnkwglhvfriaelsgnrpltvimhtifqerdllktfkip
vdtlitylmtledhyhadvayhnnihaadvvqsthvllstpaleavftdleilaaifasa
ihdvdhpgvsnqflintnselalmyndssvlenhhlavgfkllqeencdifqnltkkqrq
slrkmvidivlatdmskhmnlladlktmvetkkvtssgvllldnysdriqvlqnmvhcad
lsnptkplqlyrqwtdrimeeffrqgdrerergmeispmcdkhnasveksqvgfidyivh
plwetwadlvhpdaqdildtlednrewyqstipqspspapddpeegrqgqtekfqfeltl

    Sequence, based on observed residues (ATOM records): (download) 
    >3v9bC (C:)
qedvlakeledvnkwglhvfriaelsgnrpltvimhtifqerdllktfkipvdtlitylm
tledhyhadvayhnnihaadvvqsthvllstpaleavftdleilaaifasaihdvdhpgv
snqflintnselalmyndssvlenhhlavgfkllqeencdifqnltkkqrqslrkmvidi
vlatdmskhmnlladlktmvetkkvtssgvllldnysdriqvlqnmvhcadlsnptkplq
lyrqwtdrimeeffrqgdrerergmeispmcdkhnasveksqvgfidyivhplwetwadl
vhpdaqdildtlednrewyqstipq

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >3v9bD (D:)
iprfgvkteqedvlakeledvnkwglhvfriaelsgnrpltvimhtifqerdllktfkip
vdtlitylmtledhyhadvayhnnihaadvvqsthvllstpaleavftdleilaaifasa
ihdvdhpgvsnqflintnselalmyndssvlenhhlavgfkllqeencdifqnltkkqrq
slrkmvidivlatdmskhmnlladlktmvetkkvtssgvllldnysdriqvlqnmvhcad
lsnptkplqlyrqwtdrimeeffrqgdrerergmeispmcdkhnasveksqvgfidyivh
plwetwadlvhpdaqdildtlednrewyqstipqspspapddpeegrqgqtekfqfeltl

    Sequence, based on observed residues (ATOM records): (download) 
    >3v9bD (D:)
eqedvlakeledvnkwglhvfriaelsgnrpltvimhtifqerdllktfkipvdtlityl
mtledhyhadvayhnnihaadvvqsthvllstpaleavftdleilaaifasaihdvdhpg
vsnqflintnselalmyndssvlenhhlavgfkllqeencdifqnltkkqrqslrkmvid
ivlatdmskhmnlladlktmvetkkvtssgvllldnysdriqvlqnmvhcadlsnptkpl
qlyrqwtdrimeeffrqgdrerergmeispmcdkhnasveksqvgfidyivhplwetwad
lvhpdaqdildtlednrewyqstipq