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(-) Description

Title :  SELECTIVE INHIBITION OF THE CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 4B WITH A-33
 
Authors :  D. Fox Iii, T. E. Edwards
Date :  27 Sep 13  (Deposition) - 01 Jan 14  (Release) - 05 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Phosphodiesterase, Catalytic, Hydrolase, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Fox, A. B. Burgin, M. E. Gurney
Structural Basis For The Design Of Selective Phosphodiesterase 4B Inhibitors.
Cell Signal V. 26 657 2014
PubMed-ID: 24361374  |  Reference-DOI: 10.1016/J.CELLSIG.2013.12.003

(-) Compounds

Molecule 1 - CAMP-SPECIFIC 3',5'-CYCLIC PHOSPHODIESTERASE 4B
    Chains: A
    EC Number: 3.1.4.17
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Cell Line: SF9
    Expression System Common: FALL ARMYWORM
    Expression System Plasmid: PEMB44
    Expression System Taxid: 7108
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 324-691
    Gene: DPDE4, PDE4, PDE4B
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DPDE4, 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
119T1Ligand/Ion(4-{[2-(5-CHLOROTHIOPHEN-2-YL)-5-ETHYL-6-METHYLPYRIMIDIN-4-YL]AMINO}PHENYL)ACETIC ACID
2EDO3Ligand/Ion1,2-ETHANEDIOL
3MG1Ligand/IonMAGNESIUM ION
4NA1Ligand/IonSODIUM ION
5ZN1Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:405 , SER A:454 , ASN A:567 , ILE A:582 , PHE A:586 , MET A:603 , GLN A:615 , PHE A:618 , LEU A:674 , LYS A:677 , HOH A:849 , HOH A:867 , HOH A:911 , HOH A:967BINDING SITE FOR RESIDUE 19T A 701
2AC2SOFTWAREASP A:447 , HOH A:817 , HOH A:840 , HOH A:844 , HOH A:950 , HOH A:969BINDING SITE FOR RESIDUE MG A 702
3AC3SOFTWAREHIS A:410 , HIS A:446 , ASP A:447 , ASP A:564 , HOH A:969BINDING SITE FOR RESIDUE ZN A 703
4AC4SOFTWAREASP A:397 , TYR A:399 , SER A:401 , HOH A:871 , HOH A:1040 , HOH A:1041 , HOH A:1043BINDING SITE FOR RESIDUE NA A 704
5AC5SOFTWARELEU A:342 , GLU A:343 , ASN A:346BINDING SITE FOR RESIDUE EDO A 705
6AC6SOFTWAREPHE A:381 , ARG A:382 , ASN A:497 , GLN A:502 , HOH A:1118 , HOH A:1126BINDING SITE FOR RESIDUE EDO A 706
7AC7SOFTWAREALA A:429 , VAL A:430 , ARG A:552 , HOH A:915BINDING SITE FOR RESIDUE EDO A 707

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gln A:635 -Pro A:636

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4MYQ)

(-) 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:345
                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains d4myqa_ A: automated matches                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh....hhhhhhhhhh.......hhhhhhhh...hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhhh..hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh....hhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4myq A 324 SISRFGVNTENEDHLAKELEDLNKWGLNIFNVAGYSHNRPLTCIMYAIFQERDLLKTFRISSDTFITYMMTLEDHYHSDVAYHNSLHAADVAQSTHVLLSTPALDAVFTDLEILAAIFAAAIHDVDHPGVSNQFLINTNSELALMYNDESVLENHHLAVGFKLLQEEHCDIFMNLTKKQRQTLRKMVIDMVLATDMSKHMSLLADLKTMVETKKVTSSGVLLLDNYTDRIQVLRNMVHCADLSNPTKSLELYRQWTDRIMEEFFQQGDKERERGMEISPMCDKHTASVEKSQVGFIDYIVHPLWETWADLVQPDAQDILDTLEDNRNWYQSMIPQCQGLMEKFQF 680
                                   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    || 675     
                                                                                                                                                                                                                                                                                                                                                                        658|         
                                                                                                                                                                                                                                                                                                                                                                         671
   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 4MYQ)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (33, 33)

Asymmetric/Biological Unit(hide GO term definitions)

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  4myq
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  PDE4B_HUMAN | Q07343
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 Related Entries

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

UniProtKB/Swiss-Prot
        PDE4B_HUMAN | Q07343: 1f0j 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 3o57 3w5e 3wd9 4kp6 4nw7 4wzi 4x0f 5k6j

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4MYQ)