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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PDE5A1 CATALYTIC DOMAIN IN COMPLEX WITH NOVEL INHIBITORS
 
Authors :  J. Ren, T. Chen, Y. Xu
Date :  05 Dec 12  (Deposition) - 01 Jan 14  (Release) - 01 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.08
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Gong, G. Wang, J. Ren, Z. Liu, Z. Wang, T. Chen, X. Yang, X. Jiang, J. Shen, H. Jiang, H. A. Aisa, Y. Xu, J. Li
Exploration Of The 5-Bromopyrimidin-4(3H)-Ones As Potent Inhibitors Of Pde5.
Bioorg. Med. Chem. Lett. V. 23 4944 2013
PubMed-ID: 23867165  |  Reference-DOI: 10.1016/J.BMCL.2013.06.062

(-) Compounds

Molecule 1 - CGMP-SPECIFIC 3',5'-CYCLIC PHOSPHODIESTERASE
    Chains: A
    EC Number: 3.1.4.35
    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, 5)

Asymmetric/Biological Unit (4, 5)
No.NameCountTypeFull Name
15BA1Ligand/Ion5-BROMO-2-{5-[(4-METHYLPIPERAZIN-1-YL)ACETYL]-2-PROPOXYPHENYL}-6-(PROPAN-2-YL)PYRIMIDIN-4(3H)-ONE
2MG1Ligand/IonMAGNESIUM ION
3PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
4ZN1Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:548 , TYR A:612 , LEU A:675 , ALA A:779 , VAL A:782 , PHE A:786 , MET A:816 , GLN A:817 , PHE A:820 , ALA A:823 , PEG A:904 , HOH A:1037BINDING SITE FOR RESIDUE 5BA A 901
2AC2SOFTWAREHIS A:617 , HIS A:653 , ASP A:654 , ASP A:764 , HOH A:1004 , HOH A:1138BINDING SITE FOR RESIDUE ZN A 902
3AC3SOFTWAREASP A:654 , HOH A:1001 , HOH A:1002 , HOH A:1015 , HOH A:1137 , HOH A:1138BINDING SITE FOR RESIDUE MG A 903
4AC4SOFTWAREARG A:577 , GLY A:819 , ASP A:822 , ALA A:823 , 5BA A:901 , HOH A:1025 , HOH A:1049BINDING SITE FOR RESIDUE PEG A 904
5AC5SOFTWARESER A:562 , PHE A:564 , GLU A:565 , LEU A:690 , ASN A:694 , TYR A:709 , PRO A:773 , ARG A:777 , HOH A:1052BINDING SITE FOR RESIDUE PEG A 905

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4I9Z)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4I9Z)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4I9Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4I9Z)

(-) Exons   (0, 0)

(no "Exon" information available for 4I9Z)

(-) 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:296
                                                                                                                                                                                                                                                                                                                                        
               SCOP domains d4i9za_ A: automated matches                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh...hhhhhh...........hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i9z A 535 EETRELQSLAAAVVPSAQTLKITDFSFSDFELSDLETALCTIRMFTDLNLVQNFQMKHEVLCRWILSVKKNYRKNVAYHNWRHAFNTAQCMFAALKAGKIQNKLTDLEILALLIAALSHDLDHRGVNNSYLAQLYCHSIMEHHHFDQCLMILNSPGNQILSGLSIEEYKTTLKIIKQAILATDLALYIKRRGEFFELIRKNQFNLEDPHQKELFLAMLMTACDLSAITKPWPIQQRIAELVATEFFDKNKIPSMQVGFIDAICLQLYEALTHVSEDCFPLLDGCRKNRQKWQALAE 858
                                   544       554       564       574       584       594       604       614       624       634       644       654       664|      681       691       701       711       721       731       741       751       761       771       781      |812       822       832       842       852      
                                                                                                                                                           664|                                                                                                                 788|                                                
                                                                                                                                                            672                                                                                                                  810
   Legend:   → Mismatch (orange background)
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  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 4I9Z)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4I9Z)

(-) Gene Ontology  (22, 22)

Asymmetric/Biological Unit(hide GO term definitions)

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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 4g2y 4ia0 4md6 4oew 4oex 5jo3

(-) Related Entries Specified in the PDB File

4ia0