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(-) Description

Title :  CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 4B2B IN COMPLEX WITH A 5-HETEROCYCLE PYRAZOLOPYRIDINE INHIBITOR
 
Authors :  D. O. Somers, M. Neu
Date :  28 Jul 10  (Deposition) - 03 Aug 11  (Release) - 03 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Pde, Hydrolase, Phosphodiesterase, Camp Binding, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. J. Mitchell, S. P. Ballantine, D. M. Coe, C. M. Cook, C. J. Delves, M. D. Dowle, C. D. Edlin, J. N. Hamblin, S. Holman, M. R. Johnson, P. S. Jones, S. E. Keeling, M. Kranz, M. Lindvall, F. S. Lucas, M. Neu, Y. E. Solanke, D. O. Somers, N. A. Trivedi, J. O. Wiseman
Pyrazolopyridines As Potent Pde4B Inhibitors: 5-Heterocycle Sar.
Bioorg. Med. Chem. Lett. V. 20 5803 2010
PubMed-ID: 20732811  |  Reference-DOI: 10.1016/J.BMCL.2010.07.136

(-) Compounds

Molecule 1 - CAMP-SPECIFIC 3',5'-CYCLIC PHOSPHODIESTERASE 4B
    ChainsA
    EC Number3.1.4.17
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System CommonFALL ARMYWORM
    Expression System Taxid7108
    Expression System Vector TypeBACULOVIRUS
    FragmentCATALYTIC DOMAIN, UNP RESIDUES 324-675
    GenePDE4B, DPDE4
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymDPDE4, PDE32

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 7)

Asymmetric/Biological Unit (5, 7)
No.NameCountTypeFull Name
1ARS3Ligand/IonARSENIC
2GOL1Ligand/IonGLYCEROL
3MG1Ligand/IonMAGNESIUM ION
4ZG21Ligand/Ion5-[5-BENZYL-4-(2-OXO-2-PYRROLIDIN-1-YLETHYL)-1,3-OXAZOL-2-YL]-1-ETHYL-N-(TETRAHYDRO-2H-PYRAN-4-YL)-1H-PYRAZOLO[3,4-B]PYRIDIN-4-AMINE
5ZN1Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:71 , HIS A:238 , HIS A:274 , ASP A:275 , ASP A:392 , HOH A:516BINDING SITE FOR RESIDUE ZN A 1
2AC2SOFTWAREHOH A:69 , HOH A:70 , HOH A:71 , HOH A:72 , HOH A:75 , ASP A:275BINDING SITE FOR RESIDUE MG A 504
3AC3SOFTWAREPHE A:156 , CYS A:194BINDING SITE FOR RESIDUE ARS A 505
4AC4SOFTWARECYS A:320BINDING SITE FOR RESIDUE ARS A 2
5AC5SOFTWARESER A:429 , CYS A:432 , ZG2 A:506BINDING SITE FOR RESIDUE ARS A 3
6AC6SOFTWAREARS A:3 , HOH A:5 , HOH A:15 , HOH A:53 , TYR A:233 , SER A:282 , MET A:347 , LEU A:393 , ASN A:395 , THR A:407 , ILE A:410 , PHE A:414 , MET A:431 , GLN A:443 , GLY A:445 , PHE A:446 , HOH A:519 , HOH A:551BINDING SITE FOR RESIDUE ZG2 A 506
7AC7SOFTWARETHR A:208 , PHE A:209 , ARG A:210 , ASN A:325 , GLN A:330BINDING SITE FOR RESIDUE GOL A 507

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3O57)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gln A:463 -Pro A:464

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3O57)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDEASE_IPS00126 3'5'-cyclic nucleotide phosphodiesterases signature.PDE4B_HUMAN446-457  1A:274-285

(-) Exons   (8, 8)

Asymmetric/Biological Unit (8, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2ENST000003415172ENSE00001777645chr1:66258864-6625893168PDE4B_HUMAN-00--
1.3aENST000003415173aENSE00001454221chr1:66378928-66379039112PDE4B_HUMAN1-14140--
1.4ENST000003415174ENSE00001314677chr1:66384280-66384518239PDE4B_HUMAN15-94800--
1.10cENST0000034151710cENSE00001295605chr1:66713143-66713337195PDE4B_HUMAN94-159660--
1.12ENST0000034151712ENSE00001648425chr1:66723330-6672336637PDE4B_HUMAN159-171130--
1.13ENST0000034151713ENSE00001301262chr1:66723476-6672354671PDE4B_HUMAN172-195240--
1.14aENST0000034151714aENSE00001328762chr1:66731721-6673177050PDE4B_HUMAN195-212180--
1.17eENST0000034151717eENSE00001765348chr1:66798191-66798303113PDE4B_HUMAN212-249380--
1.19bENST0000034151719bENSE00001321190chr1:66821210-6682130394PDE4B_HUMAN250-281320--
1.21ENST0000034151721ENSE00001308616chr1:66827298-66827476179PDE4B_HUMAN281-340601A:152-16817
1.22eENST0000034151722eENSE00001292510chr1:66828851-6682894999PDE4B_HUMAN341-373331A:169-20133
1.23bENST0000034151723bENSE00001311355chr1:66829090-66829254165PDE4B_HUMAN374-428551A:202-25655
1.24ENST0000034151724ENSE00001294554chr1:66831350-66831449100PDE4B_HUMAN429-462341A:257-29034
1.25bENST0000034151725bENSE00001326709chr1:66833379-66833533155PDE4B_HUMAN462-513521A:290-34152
1.26aENST0000034151726aENSE00001304431chr1:66833626-66833748123PDE4B_HUMAN514-554411A:342-38241
1.27ENST0000034151727ENSE00001597852chr1:66834470-66834652183PDE4B_HUMAN555-615611A:383-44361
1.28cENST0000034151728cENSE00002180148chr1:66837996-668391871192PDE4B_HUMAN616-7361211A:444-48744

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:336
 aligned with PDE4B_HUMAN | Q07343 from UniProtKB/Swiss-Prot  Length:736

    Alignment length:336
                                   333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653      
          PDE4B_HUMAN   324 SISRFGVNTENEDHLAKELEDLNKWGLNIFNVAGYSHNRPLTCIMYAIFQERDLLKTFRISSDTFITYMMTLEDHYHSDVAYHNSLHAADVAQSTHVLLSTPALDAVFTDLEILAAIFAAAIHDVDHPGVSNQFLINTNSELALMYNDESVLENHHLAVGFKLLQEEHCDIFMNLTKKQRQTLRKMVIDMVLATDMSKHMSLLADLKTMVETKKVTSSGVLLLDNYTDRIQVLRNMVHCADLSNPTKSLELYRQWTDRIMEEFFQQGDKERERGMEISPMCDKHTASVEKSQVGFIDYIVHPLWETWADLVQPDAQDILDTLEDNRNWYQSMIPQS 659
               SCOP domains d3o57a_ A: Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhh.......hhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhh...hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------PDEASE_I    ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.21        Exon 1.22e  PDB: A:169-201       Exon 1.23b  PDB: A:202-256 UniProt: 374-428            Exon 1.24  PDB: A:257-290         ---------------------------------------------------Exon 1.26a  PDB: A:342-382               Exon 1.27  PDB: A:383-443 UniProt: 555-615                   Exon 1.28c  PDB: A:444-487 UniProt: 616-736  Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------------------------------------------------------Exon 1.25b  PDB: A:290-341 UniProt: 462-513         -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3o57 A 152 SISRFGVNTENEDHLAKELEDLNKWGLNIFNVAGYSHNRPLTCIMYAIFQERDLLKTFRISSDTFITYMMTLEDHYHSDVAYHNSLHAADVAQSTHVLLSTPALDAVFTDLEILAAIFAAAIHDVDHPGVSNQFLINTNSELALMYNDESVLENHHLAVGFKLLQEEHCDIFMNLTKKQRQTLRKMVIDMVLATDMSKHMSLLADLKTMVETKKVTSSGVLLLDNYTDRIQVLRNMVHCADLSNPTKSLELYRQWTDRIMEEFFQQGDKERERGMEISPMCDKHTASVEKSQVGFIDYIVHPLWETWADLVQPDAQDILDTLEDNRNWYQAMIPQA 487
                                   161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481      

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3O57)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3O57)

(-) Gene Ontology  (33, 33)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PDE4B_HUMAN | Q07343)
molecular function
    GO:0004115    3',5'-cyclic-AMP phosphodiesterase activity    Catalysis of the reaction: adenosine 3',5'-cyclic phosphate + H2O = adenosine 5'-phosphate.
    GO:0004114    3',5'-cyclic-nucleotide phosphodiesterase activity    Catalysis of the reaction: nucleoside 3',5'-cyclic phosphate + H2O = nucleoside 5'-phosphate.
    GO:0030552    cAMP binding    Interacting selectively and non-covalently with cAMP, the nucleotide cyclic AMP (adenosine 3',5'-cyclophosphate).
    GO:0043015    gamma-tubulin binding    Interacting selectively and non-covalently with the microtubule constituent protein gamma-tubulin.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0044325    ion channel binding    Interacting selectively and non-covalently with one or more specific sites on an ion channel, a protein complex that spans a membrane and forms a water-filled channel across the phospholipid bilayer allowing selective ion transport down its electrochemical gradient.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008081    phosphoric diester hydrolase activity    Catalysis of the hydrolysis of a phosphodiester to give a phosphomonoester and a free hydroxyl group.
biological process
    GO:0050852    T cell receptor signaling pathway    A series of molecular signals initiated by the cross-linking of an antigen receptor on a T cell.
    GO:0006198    cAMP catabolic process    The chemical reactions and pathways resulting in the breakdown of the nucleotide cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate).
    GO:0035690    cellular response to drug    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    GO:0071872    cellular response to epinephrine stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an epinephrine stimulus. Epinephrine is a catecholamine that has the formula C9H13NO3; it is secreted by the adrenal medulla to act as a hormone, and released by certain neurons to act as a neurotransmitter active in the central nervous system.
    GO:0071222    cellular response to lipopolysaccharide    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
    GO:0050900    leukocyte migration    The movement of a leukocyte within or between different tissues and organs of the body.
    GO:1901898    negative regulation of relaxation of cardiac muscle    Any process that stops, prevents or reduces the frequency, rate or extent of relaxation of cardiac muscle.
    GO:0030593    neutrophil chemotaxis    The directed movement of a neutrophil cell, the most numerous polymorphonuclear leukocyte found in the blood, in response to an external stimulus, usually an infection or wounding.
    GO:0001780    neutrophil homeostasis    The process of regulating the proliferation and elimination of neutrophils such that the total number of neutrophils within a whole or part of an organism is stable over time in the absence of an outside stimulus.
    GO:0032729    positive regulation of interferon-gamma production    Any process that activates or increases the frequency, rate, or extent of interferon-gamma production. Interferon-gamma is also known as type II interferon.
    GO:0032743    positive regulation of interleukin-2 production    Any process that activates or increases the frequency, rate, or extent of interleukin-2 production.
    GO:0086004    regulation of cardiac muscle cell contraction    Any process that modulates the frequency, rate or extent of cardiac muscle cell contraction.
    GO:1901841    regulation of high voltage-gated calcium channel activity    Any process that modulates the frequency, rate or extent of high voltage-gated calcium channel activity.
    GO:0007165    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.
cellular component
    GO:0030018    Z disc    Platelike region of a muscle sarcomere to which the plus ends of actin filaments are attached.
    GO:0071944    cell periphery    The part of a cell encompassing the cell cortex, the plasma membrane, and any external encapsulating structures.
    GO:0005813    centrosome    A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0043197    dendritic spine    A small, membranous protrusion from a dendrite that forms a postsynaptic compartment - typically receiving input from a single presynapse. They function as partially isolated biochemical and an electrical compartments. Spine morphology is variable including "thin", "stubby", "mushroom", and "branched", with a continuum of intermediate morphologies. They typically terminate in a bulb shape, linked to the dendritic shaft by a restriction. Spine remodeling is though to be involved in synaptic plasticity.
    GO:0060076    excitatory synapse    A synapse in which an action potential in the presynaptic cell increases the probability of an action potential occurring in the postsynaptic cell.
    GO:0000930    gamma-tubulin complex    A multiprotein complex composed of gamma-tubulin and other non-tubulin proteins. Gamma-tubulin complexes are localized to microtubule organizing centers, and play an important role in the nucleation of microtubules. The number and complexity of non-tubulin proteins associated with these complexes varies between species.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0014069    postsynaptic density of dendrite    An electron dense network of proteins within and adjacent to the postsynaptic membrane of the dendrite of asymetric synapses. Its major components include neurotransmitter receptors and the proteins that spatially and functionally organize them such as anchoring and scaffolding molecules, signaling enzymes and cytoskeletal components.
    GO:0008021    synaptic vesicle    A secretory organelle, typically 50 nm in diameter, of presynaptic nerve terminals; accumulates in high concentrations of neurotransmitters and secretes these into the synaptic cleft by fusion with the 'active zone' of the presynaptic plasma membrane.
    GO:0005891    voltage-gated calcium channel complex    A protein complex that forms a transmembrane channel through which calcium ions may pass in response to changes in membrane potential.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PDE4B_HUMAN | Q073431f0j 1jp1 1jp2 1ro6 1ro9 1ror 1tb5 1xlx 1xlz 1xm4 1xm6 1xmu 1xmy 1xn0 1xos 1xot 1y2h 1y2j 2chm 2qyl 3d3p 3frg 3g45 3gwt 3hc8 3hdz 3hmv 3kkt 3ly2 3o0j 3o56 3w5e 3wd9 4kp6 4myq 4nw7 4wzi 4x0f 5k6j

(-) Related Entries Specified in the PDB File

3d3p CRYSTAL STRUCTURE OF PDE4B CATALYTIC DOMAIN IN COMPLEX WITH A PYRAZOLOPYRIDINE INHIBITOR
3o56 CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 4B2B IN COMPLEX WITH A 5-HETEROCYCLE PYRAZOLOPYRIDINE INHIBITOR