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(-) Description

Title :  CRYSTAL STRUCTURE OF N2 SUBSTITUTED PYRAZOLO PYRIMIDINONES-A FLIPPED BINDING MODE IN PDE5
 
Authors :  C. M. N. Allerton, C. G. Barber, K. C. Beaumont, D. G. Brown, S. M. Cole, D. Ellis, C. A. L. Lane, G. N. Maw, N. M. Mount, D. J. Rawson, C. M. Robinson, S. D. A. Street, N. W. Summerhill
Date :  15 Mar 06  (Deposition) - 08 Jun 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Phosphodiesterase 5, Inhibitor, Chimera, Allosteric Enzyme, Alternative Splicing, Cgmp, Cgmp-Binding, Hydrolase, Magnesium, Metal-Binding, Nucleotide-Binding, Phosphorylation, Zinc, Camp (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. M. N. Allerton, C. G. Barber, K. C. Beaumont, D. G. Brown, S. M. Cole, D. Ellis, C. A. L. Lane, G. N. Maw, N. M. Mount, D. J. Rawson, C. M. Robinson, S. D. A. Street, N. W. Summerhill
A Novel Series Of Potent And Selective Pde5 Inhibitors With Potential For High And Dose- Independent Oral Bioavailability
J. Med. Chem. V. 49 3581 2006
PubMed-ID: 16759100  |  Reference-DOI: 10.1021/JM060113E

(-) Compounds

Molecule 1 - CGMP-SPECIFIC 3', 5'-CYCLIC PHOSPHODIESTERASE, CAMP-SPECIFIC 3', 5'-CYCLIC PHOSPHODIESTERASE 4B
    ChainsA
    EC Number3.1.4.17, 3.1.4.35
    EngineeredYES
    Expression SystemTRICHOPLUSIA NI
    Expression System PlasmidFASTBAC
    Expression System StrainHIGH5
    Expression System Taxid7111
    Expression System Vector TypeBACULOVIRUS
    FragmentCATALYTIC DOMAIN RESIDUES (RESIDUES 534-858 WITH SUBDOMAIN REPLACED WITH PDE4 SUBDOMAIN)
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other Details5-(5-ACETYL-2-BUTOXY-3-PYRIDINYL)-3-ETHYL-2 -(1-ETHYL-3-AZETIDINYL)-2,6-DIHYDRO-7H-PYRAZOLO (4,3-D) PYRIMIDIN-7-ONE
    Synonym3', 5' CGMP-CYCLIC PHOPHODIESTERASE 5A CATALYTIC DOMAIN CHIMERA, CGB-PDE, CGMP-BINDING CGMP-SPECIFIC PHOSPHODIESTERASE, DPDE4, PDE32

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 4)

Asymmetric/Biological Unit (4, 4)
No.NameCountTypeFull Name
13P41Ligand/Ion5-[2-(BUT-3-EN-1-YLOXY)-5-(1-HYDROXYVINYL)PYRIDIN-3-YL]-3-ETHYL-2-(1-ETHYLAZETIDIN-3-YL)-1,2,6,7A-TETRAHYDRO-7H-PYRAZOLO[4,3-D]PYRIMIDIN-7-ONE
2MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3MG1Ligand/IonMAGNESIUM ION
4ZN1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:617 , HIS A:653 , ASP A:654 , ASP A:764 , HOH A:2508 , HOH A:2509BINDING SITE FOR RESIDUE ZN A1859
2AC2SOFTWAREASP A:654 , HOH A:2118 , HOH A:2182 , HOH A:2222 , HOH A:2223 , HOH A:2508BINDING SITE FOR RESIDUE MG A1860
3AC3SOFTWAREALA A:545 , LEU A:725 , LEU A:765 , ALA A:767 , ILE A:768 , GLN A:775 , ALA A:779 , VAL A:782 , ALA A:783 , LEU A:804 , MET A:816 , GLN A:817 , PHE A:820 , HOH A:2510 , HOH A:2511 , HOH A:2512BINDING SITE FOR RESIDUE 3P4 A1861
4AC4SOFTWAREARG A:607 , LYS A:608 , ASN A:609 , ASN A:742 , GLN A:743 , PHE A:744 , ASN A:745 , HOH A:2154 , HOH A:2513 , HOH A:2514 , HOH A:2515BINDING SITE FOR RESIDUE MES A1862

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2CHM)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2CHM)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2CHM)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDEASE_IPS00126 3'5'-cyclic nucleotide phosphodiesterases signature.PDE5A_HUMAN653-664  1A:653-662

(-) Exons   (11, 11)

Asymmetric/Biological Unit (11, 11)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003549601aENSE00001851914chr4:120550146-120549675472PDE5A_HUMAN1-51510--
1.4ENST000003549604ENSE00001637089chr4:120528452-120527864589PDE5A_HUMAN51-2471970--
1.5bENST000003549605bENSE00000935544chr4:120517767-12051767890PDE5A_HUMAN248-277300--
1.6ENST000003549606ENSE00000970323chr4:120488299-12048822872PDE5A_HUMAN278-301240--
1.7ENST000003549607ENSE00000970324chr4:120486565-12048647690PDE5A_HUMAN302-331300--
1.8bENST000003549608bENSE00000970325chr4:120484125-120483988138PDE5A_HUMAN332-377460--
1.9ENST000003549609ENSE00000970326chr4:120481518-12048145168PDE5A_HUMAN378-400230--
1.10ENST0000035496010ENSE00000970327chr4:120474901-120474793109PDE5A_HUMAN400-436370--
1.11aENST0000035496011aENSE00000970328chr4:120473792-12047370588PDE5A_HUMAN437-466300--
1.13ENST0000035496013ENSE00000935541chr4:120463789-120463614176PDE5A_HUMAN466-524590--
1.15bENST0000035496015bENSE00000935545chr4:120460174-12046011560PDE5A_HUMAN525-544201A:537-5448
1.18ENST0000035496018ENSE00001016848chr4:120446850-120446704147PDE5A_HUMAN545-593491A:545-59349
1.19bENST0000035496019bENSE00001016844chr4:120442215-120442090126PDE5A_HUMAN594-635421A:594-63542
1.20cENST0000035496020cENSE00001016846chr4:120440294-12044020095PDE5A_HUMAN636-667321A:636-66732
1.22ENST0000035496022ENSE00001016843chr4:120432289-12043220288PDE5A_HUMAN667-696301A:667-69631
1.23bENST0000035496023bENSE00001016840chr4:120428859-120428759101PDE5A_HUMAN697-730341A:697-73034
1.24bENST0000035496024bENSE00001016847chr4:120427087-12042701078PDE5A_HUMAN730-756271A:730-75627
1.25ENST0000035496025ENSE00001016842chr4:120425754-12042569164PDE5A_HUMAN756-777221A:756-77722
1.26aENST0000035496026aENSE00001016841chr4:120423810-12042373675PDE5A_HUMAN778-802251A:778-80225
1.27aENST0000035496027aENSE00001016845chr4:120422408-12042232584PDE5A_HUMAN803-830281A:803-83028
1.28cENST0000035496028cENSE00001890486chr4:120419893-1204155504344PDE5A_HUMAN831-875451A:831-85828

(-) 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:323
 aligned with PDE5A_HUMAN | O76074 from UniProtKB/Swiss-Prot  Length:875

    Alignment length:323
                                                                                                                                                                         679                                                                                                                                                                                   
                                                                                                                                                                       678 |                                                                                                                                                                                   
                                   546       556       566       576       586       596       606       616       626       636       646       656       666       676 | |   685       695       705       715       725       735       745       755       765       775       785       795       805       815       825       835       845       855   
         PDE5A_HUMAN    537 TRELQSLAAAVVPSAQTLKITDFSFSDFELSDLETALCTIRMFTDLNLVQNFQMKHEVLCRWILSVKKNYRKNVAYHNWRHAFNTAQCMFAALKAGKIQNKLTDLEILALLIAALSHDLDHRGVNNSYIQRSEHPLAQLYCH-SIMEHHHFDQCLMILNSPGNQILSGLSIEEYKTTLKIIKQAILATDLALYIKRRGEFFELIRKNQFNLEDPHQKELFLAMLMTACDLSAITKPWPIQQRIAELVATEFFDQGDRERKELNIEPTDLMNREKKNKIPSMQVGFIDAICLQLYEALTHVSEDCFPLLDGCRKNRQKWQALAE  858
               SCOP domains d2chma1 A:537-858 cGMP-specific 3',5'-cyclic phosphodiesterase pde5a1-Ibmx                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 2chmA00 A:537-858 Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b                                                                                                                                                                                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh...hhhhhh...........hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhh...hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------PDEASE_I    --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.15b   Exon 1.18  PDB: A:545-593 UniProt: 545-593       Exon 1.19b  PDB: A:594-635                Exon 1.20c  PDB: A:636-667      ------------------------------Exon 1.23b  PDB: A:697-730        -------------------------Exon 1.25             Exon 1.26a  PDB: A:778-80Exon 1.27a  PDB: A:803-830  Exon 1.28c  PDB: A:831-858   Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------------------------------------------------Exon 1.22  PDB: A:667-696      ---------------------------------Exon 1.24b  PDB: A:730-756 ------------------------------------------------------------------------------------------------------ Transcript 1 (2)
                2chm A  537 TRELQSLAAAVVPSAQTLKITDFSFSDFELSDLETALCTIRMFTDLNLVQNFQMKHEVLCRWILSVKKNYRKNVAYHNWRHAFNTAQCMFAALKAGKIQNKLTDLEILALLIAALSHDLDHPGVSNQFLINTNSELALMYNDESVLEHHHFDQCLMILNSPGNQILSGLSIEEYKTTLKIIKQAILATDLALYIKRRGEFFELIRKNQFNLEDPHEKELFLAMLMTACDLSAITKPWPIQQRIAELVATEFFDQGDRERKELNIEPTDLMNREKKNKIPSMQVGFIDAICLQLYEALTHVSEDCFPLLDGCRKNRQKWQALAE  858
                                   546       556       566       576       586       596       606       616       626       636       646       656       666       676     | 685       695       705       715       725       735       745       755       765       775       785       795       805       815       825       835       845       855   
                                                                                                                                                                          681A                                                                                                                                                                                 

   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  (1, 1)

Asymmetric/Biological Unit

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2CHM)

(-) Gene Ontology  (49, 55)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PDE5A_HUMAN | O76074)
molecular function
    GO:0047555    3',5'-cyclic-GMP phosphodiesterase activity    Catalysis of the reaction: guanosine 3',5'-cyclic phosphate + H2O = guanosine 5'-phosphate.
    GO:0004114    3',5'-cyclic-nucleotide phosphodiesterase activity    Catalysis of the reaction: nucleoside 3',5'-cyclic phosphate + H2O = nucleoside 5'-phosphate.
    GO:0030553    cGMP binding    Interacting selectively and non-covalently with cGMP, the nucleotide cyclic GMP (guanosine 3',5'-cyclophosphate).
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0004112    cyclic-nucleotide phosphodiesterase activity    Catalysis of the reaction: a nucleoside cyclic phosphate + H2O = a nucleoside phosphate.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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:0046069    cGMP catabolic process    The chemical reactions and pathways resulting in the breakdown of cyclic GMP, guanosine 3',5'-phosphate.
    GO:0046068    cGMP metabolic process    The chemical reactions and pathways involving cyclic GMP, guanosine 3',5'-phosphate.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0042130    negative regulation of T cell proliferation    Any process that stops, prevents or reduces the rate or extent of T cell proliferation.
    GO:0055118    negative regulation of cardiac muscle contraction    Any process that stops, prevents, or reduces the frequency, rate or extent of cardiac muscle contraction.
    GO:0043406    positive regulation of MAP kinase activity    Any process that activates or increases the frequency, rate or extent of MAP kinase activity.
    GO:0010613    positive regulation of cardiac muscle hypertrophy    Any process that increases the rate, frequency or extent of the enlargement or overgrowth of all or part of the heart due to an increase in size (not length) of individual cardiac muscle fibers, without cell division.
    GO:0060282    positive regulation of oocyte development    Any process that increases the rate or extent of the process whose specific outcome is the progression of an oocyte over time, from initial commitment of the cell to its specific fate, to the fully functional differentiated cell.
    GO:0030823    regulation of cGMP metabolic process    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving cGMP.
    GO:0055119    relaxation of cardiac muscle    The process in which the extent of cardiac muscle contraction is reduced.
    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:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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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 2qyl 3d3p 3frg 3g45 3gwt 3hc8 3hdz 3hmv 3kkt 3ly2 3o0j 3o56 3o57 3w5e 3wd9 4kp6 4myq 4nw7 4wzi 4x0f 5k6j
        PDE5A_HUMAN | O760741rkp 1t9r 1t9s 1tbf 1udt 1udu 1uho 1xoz 1xp0 2h40 2h42 2h44 2xss 3b2r 3bjc 3hc8 3hdz 3jwq 3jwr 3lfv 3mf0 3shy 3shz 3sie 3tge 3tgg 4g2w 4g2y 4i9z 4ia0 4md6 4oew 4oex 5jo3

(-) Related Entries Specified in the PDB File

1f0j CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 4B2B
1jp1 MOLECULAR DOCKING OF COMPETITIVE PHOSPHODIESTERASESUBSTRATE CYCLIC ADENOSINE 3',5 '-MONOPHOSPHATE (CAMP)
1jp2 MOLECULAR DOCKING OF COMPETITIVE PHOSPHODIESTERASEINHIBITOR, 4-[3-(CYCLOPENTYLOXY )-4-METHOXYPHENYL]-2-PYRROLIDINONE, ROLIPRAM
1rkp CRYSTAL STRUCTURE OF PDE5A1-IBMX
1ro6 CRYSTAL STRUCTURE OF PDE4B2B COMPLEXED WITH ROLIPRAM (R & S)
1ro9 CRYSTAL STRUCTURES OF THE CATALYTIC DOMAIN OFPHOSPHODIESTERASE 4B2B COMPLEXED WITH 8-BR- AMP
1ror CRYSTAL STRUCTURES OF THE CATALYTIC DOMAIN OFPHOSPHODIESTERASE 4B2B COMPLEXED WITH AMP
1t9r CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 5A
1t9s CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 5A IN COMPLEXWITH GMP
1tb5 CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 4B IN COMPLEXWITH AMP
1tbf CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 5A IN COMPLEXWITH SILDENAFIL
1udt CRYSTAL STRUCTURE OF HUMAN PHOSPHODIESTERASE 5 COMPLEXEDWITH SILDENAFIL(VIAGRA)
1udu CRYSTAL STRUCTURE OF HUMAN PHOSPHODIESTERASE 5 COMPLEXEDWITH TADALAFIL(CIALIS)
1uho CRYSTAL STRUCTURE OF HUMAN PHOSPHODIESTERASE 5 COMPLEXEDWITH VARDENAFIL(LEVITRA)
1xlx CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 4B IN COMPLEXWITH CILOMILAST
1xlz CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 4B IN COMPLEXWITH FILAMINAST
1xm4 CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 4B IN COMPLEXWITH PICLAMILAST
1xm6 CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 4B IN COMPLEXWITH (R)-MESOPRAM
1xmu CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 4B IN COMPLEXWITH ROFLUMILAST
1xmy CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 4B IN COMPLEXWITH (R)-ROLIPRAM
1xn0 CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 4B IN COMPLEXWITH (R,S)-ROLIPRAM
1xos CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 4B IN COMPLEXWITH SILDENAFIL
1xot CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 4B IN COMPLEXWITH VARDENAFIL
1xoz CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 5A IN COMPLEXWITH TADALAFIL
1xp0 CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 5A IN COMPLEXWITH VARDENAFIL
1y2h CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 4B IN COMPLEXWITH 1-(2-CHLORO-PHENYL)-3,5- DIMETHYL-1H-PYRAZOLE-4-CARBOXYLIC ACID ETHYL ESTER
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