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(-) Description

Title :  CRYSTAL STRUCTURE OF PDE5A COMPLEXED WITH ITS INHIBITOR
 
Authors :  J. Ren, T. T. Chen, Y. C. Xu
Date :  13 Jul 12  (Deposition) - 26 Jun 13  (Release) - 26 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Phosphodiesterase, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Wang, Z. Liu, T. T. Chen, Z. Wang, H. Yang, M. Zheng, J. Ren, G. Tian, X. Yang, L. Li, J. Li, J. Suo, R. Zhang, X. Jiang, N. K. Terrett, J. Shen, Y. C. Xu, H. Jiang
Design, Synthesis, And Pharmacological Evaluation Of Monocyclic Pyrimidinones As Novel Inhibitors Of Pde5.
J. Med. Chem. V. 55 10540 2012
PubMed-ID: 23137303  |  Reference-DOI: 10.1021/JM301159Y

(-) Compounds

Molecule 1 - CGMP-SPECIFIC 3',5'-CYCLIC PHOSPHODIESTERASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 535-860
    Gene: PDE5, PDE5A
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CGMP-BINDING CGMP-SPECIFIC PHOSPHODIESTERASE, CGB-PDE

 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
1MG1Ligand/IonMAGNESIUM ION
2NI51Ligand/Ion2-{5-[(4-METHYLPIPERAZIN-1-YL)SULFONYL]-2-PROPOXYPHENYL}-3,5,6,7-TETRAHYDRO-4H-CYCLOPENTA[D]PYRIMIDIN-4-ONE
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
4ZN1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:657 , GLU A:682 , ASP A:724 , HOH A:1020 , HOH A:1055BINDING SITE FOR RESIDUE PEG A 901
2AC2SOFTWAREHIS A:617 , HIS A:653 , ASP A:654 , ASP A:764 , MG A:903 , HOH A:1009 , HOH A:1065BINDING SITE FOR RESIDUE ZN A 902
3AC3SOFTWAREASP A:654 , ZN A:902 , HOH A:1001 , HOH A:1004 , HOH A:1055 , HOH A:1057 , HOH A:1065BINDING SITE FOR RESIDUE MG A 903
4AC4SOFTWARETYR A:612 , LEU A:672 , LEU A:725 , ALA A:779 , PHE A:786 , GLN A:817 , PHE A:820 , ILE A:824BINDING SITE FOR RESIDUE NI5 A 904

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4G2Y)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ala A:673 -Gln A:674

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4G2Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4G2Y)

(-) Exons   (0, 0)

(no "Exon" information available for 4G2Y)

(-) 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:297
                                                                                                                                                                                                                                                                                                                                         
               SCOP domains d4g2ya_ A: automated matches                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh...hhhhhh...........hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4g2y A 534 MEETRELQSLAAAVVPSAQTLKITDFSFSDFELSDLETALCTIRMFTDLNLVQNFQMKHEVLCRWILSVKKNYRKNVAYHNWRHAFNTAQCMFAALKAGKIQNKLTDLEILALLIAALSHDLDHRGVNNSPLAQLYCHSIMEHHHFDQCLMILNSPGNQILSGLSIEEYKTTLKIIKQAILATDLALYIKRRGEFFELIRKNQFNLEDPHQKELFLAMLMTACDLSAITKPWPIQQRIAELVATEFFDKNKIPSMQVGFIDAICLQLYEALTHVSEDCFPLLDGCRKNRQKWQALAE 858
                                   543       553       563       573       583       593       603       613       623       633       643       653       663|      680       690       700       710       720       730       740       750       760       770       780       811       821       831       841       851       
                                                                                                                                                           663|                                                                                                                  788|                                                
                                                                                                                                                            671                                                                                                                   810
   Legend:   → Mismatch (orange background)
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    → 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
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4G2Y)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4G2Y)

(-) Gene Ontology  (22, 22)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala A:673 - Gln A:674   [ RasMol ]  
 

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  PDE5A_HUMAN | O76074
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 Related Entries

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

UniProtKB/Swiss-Prot
        PDE5A_HUMAN | O76074: 1rkp 1t9r 1t9s 1tbf 1udt 1udu 1uho 1xoz 1xp0 2chm 2h40 2h42 2h44 2xss 3b2r 3bjc 3hc8 3hdz 3jwq 3jwr 3lfv 3mf0 3shy 3shz 3sie 3tge 3tgg 4g2w 4i9z 4ia0 4md6 4oew 4oex 5jo3

(-) Related Entries Specified in the PDB File

4g2w