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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PDE5A1 CATALYTIC DOMAIN IN COMPLEX WITH NOVEL INHIBITORS
 
Authors :  T. T. Chen, J. Ren, Y. C. Xu
Date :  14 Jan 14  (Deposition) - 01 Apr 15  (Release) - 01 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.14
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Ren, Y. He, W. Chen, T. Chen, G. Wang, Z. Wang, Z. Xu, X. Luo, W. Zhu, H. Jiang, J. Shen, Y. Xu
Thermodynamic And Structural Characterization Of Halogen Bonding In Protein-Ligand Interactions: A Case Study Of Pde And Its Inhibitors.
J. Med. Chem. V. 57 3588 2014
PubMed-ID: 24702184  |  Reference-DOI: 10.1021/JM5002315

(-) 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: 469008
    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  (3, 3)

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
15EO1Ligand/Ion6-ETHYL-2-{5-[(4-METHYLPIPERAZIN-1-YL)SULFONYL]-2-PROPOXYPHENYL}PYRIMIDIN-4(3H)-ONE
2MG1Ligand/IonMAGNESIUM ION
3ZN1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:667 , ALA A:779 , VAL A:782 , PHE A:786 , GLN A:817 , PHE A:820 , ILE A:824 , HOH A:1089 , HOH A:1154BINDING SITE FOR RESIDUE 5EO A 901
2AC2SOFTWAREHIS A:617 , HIS A:653 , ASP A:654 , ASP A:764 , HOH A:1002 , HOH A:1003BINDING SITE FOR RESIDUE ZN A 902
3AC3SOFTWAREASP A:654 , HOH A:1002 , HOH A:1004 , HOH A:1086 , HOH A:1093 , HOH A:1115BINDING SITE FOR RESIDUE MG A 903

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gln A:789 -Gly A:790

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4OEX)

(-) 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 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh....................hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4oex A 534 MEETRELQSLAAAVVPSAQTLKITDFSFSDFELSDLETALCTIRMFTDLNLVQNFQMKHEVLCRWILSVKKNYRKNVAYHNWRHAFNTAQCMFAALKAGKIQNKLTDLEILALLIAALSHDLDHRGVNNSYIQRSIMEHHHFDQCLMILNSPGNQILSGLSIEEYKTTLKIIKQAILATDLALYIKRRGEFFELIRKNQFNLEDPHQKELFLAMLMTACDLSAITKPWPIQQRIAELVATEFFDQGKNKIPSMQVGFIDAICLQLYEALTHVSEDCFPLLDGCRKNRQKWQALAEQQ 860
                                   543       553       563       573       583       593       603       613       623       633       643       653       663   ||  684       694       704       714       724       734       744       754       764       774       784     ||813       823       833       843       853       
                                                                                                                                                               667|                                                                                                            790|                                                  
                                                                                                                                                                679                                                                                                             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  (0, 0 ; only for superseded entry 3TSE: 1,1)

(no "SCOP Domain" information available for 4OEX, only for superseded entry 3TSE replaced by 4OEX)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (22, 22)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Gln A:789 - Gly A:790   [ RasMol ]  
 

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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 4i9z 4ia0 4md6 4oew 5jo3

(-) Related Entries Specified in the PDB File

4oew