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(-) Description

Title :  PDE4D COMPLEXED WITH INHIBITOR
 
Authors :  M. D. Sorensen
Date :  14 Aug 14  (Deposition) - 05 Nov 14  (Release) - 05 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Inhibitor, Complex, Pde4D, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Felding, M. D. Sorensen, T. D. Poulsen, J. Larsen, C. Andersson, P. Refer, K. Engell, L. G. Ladgefoged, T. Thormann, A. M. Vinggaard, P. Hegardt, A. Sohoel, S. F. Nielse
Discovery And Early Clinical Development Of 2-{6-[2-(3, 5-Dichloro-4-Pyridyl)Acetyl]-2, 3-Dimethoxyphenoxy}-N-Propylacetamide (Leo 29102), A Soft-Drug Inhibitor Of Phosphodiesterase 4 For Topical Treatment Of Atopic Dermatitis
J. Med. Chem V. 57 5893 2014
PubMed-ID: 24984230  |  Reference-DOI: 10.1021/JM500378A

(-) Compounds

Molecule 1 - CAMP-SPECIFIC 3',5'-CYCLIC PHOSPHODIESTERASE 4D
    ChainsA, B, C, D
    EC Number3.1.4.53
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GenePDE4D, DPDE3
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymDPDE3,PDE43

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric/Biological Unit (2, 12)
No.NameCountTypeFull Name
13GJ4Ligand/IonN-(3,5-DICHLOROPYRIDIN-4-YL)-3-[(3-ETHYL-1,2-OXAZOL-5-YL)METHOXY]-4-METHOXYBENZAMIDE
2ZN8Ligand/IonZINC ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:159 , HIS A:160 , THR A:271 , MET A:273 , ASP A:318 , LEU A:319 , ASN A:321 , THR A:333 , ILE A:336 , MET A:357 , SER A:368 , GLN A:369 , PHE A:372 , HOH A:727 , HOH A:728 , HOH A:743binding site for residue 3GJ A 501
02AC2SOFTWAREHIS A:164 , HIS A:200 , ASP A:201 , ASP A:318binding site for residue ZN A 502
03AC3SOFTWAREASP A:201 , HOH A:742 , HOH A:743 , HOH A:744binding site for residue ZN A 503
04AC4SOFTWARETYR B:159 , HIS B:160 , THR B:271 , MET B:273 , ASP B:318 , LEU B:319 , ASN B:321 , TYR B:329 , THR B:333 , ILE B:336 , MET B:357 , SER B:368 , GLN B:369 , PHE B:372 , HOH B:640 , HOH B:711 , HOH B:715 , HOH B:721binding site for residue 3GJ B 501
05AC5SOFTWAREHIS B:164 , HIS B:200 , ASP B:201 , ASP B:318binding site for residue ZN B 502
06AC6SOFTWAREASP B:201 , HOH B:719 , HOH B:720 , HOH B:721binding site for residue ZN B 503
07AC7SOFTWARETYR C:159 , HIS C:160 , THR C:271 , MET C:273 , ASP C:318 , LEU C:319 , TYR C:329 , ILE C:336 , MET C:357 , SER C:368 , GLN C:369 , PHE C:372 , HOH C:693 , HOH C:698 , HOH C:700binding site for residue 3GJ C 501
08AC8SOFTWAREHIS C:164 , HIS C:200 , ASP C:201 , ASP C:318binding site for residue ZN C 502
09AC9SOFTWAREASP C:201 , HOH C:698 , HOH C:699 , HOH C:700 , HOH C:701binding site for residue ZN C 503
10AD1SOFTWARETYR D:159 , THR D:271 , MET D:273 , ASP D:318 , LEU D:319 , ASN D:321 , THR D:333 , ILE D:336 , MET D:357 , SER D:368 , GLN D:369 , PHE D:372 , HOH D:691binding site for residue 3GJ D 501
11AD2SOFTWAREHIS D:164 , HIS D:200 , ASP D:201 , ASP D:318binding site for residue ZN D 502
12AD3SOFTWAREASP D:201 , HOH D:701 , HOH D:702 , HOH D:703binding site for residue ZN D 503

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4W1O)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1His A:389 -Pro A:390
2His B:389 -Pro B:390
3His C:389 -Pro C:390
4His D:389 -Pro D:390

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4W1O)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4W1O)

(-) Exons   (0, 0)

(no "Exon" information available for 4W1O)

(-) 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:322
                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh...hhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhh...hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4w1o A  90 DVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQERDLLKTFKIPVDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPALEAVFTDLEILAAIFASAIHDVDHPGVSNQFLINTNSELALMYNDSSVLENHHLAVGFKLLQEENCDIFQNLTKKQRQSLRKMVIDIVLATDMSKHMNLLADLKTMVETKKVTSSGVLLLDNYSDRIQVLQNMVHCADLSNPTKPLQLYRQWTDRIMEEFFRQGDRERERGMEISPMCDKHNASVEKSQVGFIDYIVHPLWETWADLVHPDAQDILDTLEDNREWYQSTIP 411
                                    99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409  

Chain B from PDB  Type:PROTEIN  Length:325
                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhh.....hhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhh...hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4w1o B  83 GVKTEQEDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQERDLLKTFKIPVDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPALEAVFTDLEILAAIFASAIHDVDHPGVSNQFLINTNSELALMYNDSSVLENHHLAVGFKLLQEENCDIFQNLTKKQRQSLRKMVIDIVLATDMSKHMNLLADLKTMVETKKVVLLLDNYSDRIQVLQNMVHCADLSNPTKPLQLYRQWTDRIMEEFFRQGDRERERGMEISPMCDKHNASVEKSQVGFIDYIVHPLWETWADLVHPDAQDILDTLEDNREWYQSTIP 411
                                    92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292|      306       316       326       336       346       356       366       376       386       396       406     
                                                                                                                                                                                                                                           292|                                                                                                                  
                                                                                                                                                                                                                                            297                                                                                                                  

Chain C from PDB  Type:PROTEIN  Length:321
                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh...hhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhhh..hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4w1o C  87 EQEDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQERDLLKTFKIPVDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPALEAVFTDLEILAAIFASAIHDVDHPGVSNQFLINTNSELALMYNDSSVLENHHLAVGFKLLQEENCDIFQNLTKKQRQSLRKMVIDIVLATDMSKHMNLLADLKTMVETKKVVLLLDNYSDRIQVLQNMVHCADLSNPTKPLQLYRQWTDRIMEEFFRQGDRERERGMEISPMCDKHNASVEKSQVGFIDYIVHPLWETWADLVHPDAQDILDTLEDNREWYQSTIP 411
                                    96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286     ||300       310       320       330       340       350       360       370       380       390       400       410 
                                                                                                                                                                                                                                       292|                                                                                                                  
                                                                                                                                                                                                                                        297                                                                                                                  

Chain D from PDB  Type:PROTEIN  Length:317
                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh.....hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhhh..hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4w1o D  91 VLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQERDLLKTFKIPVDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPALEAVFTDLEILAAIFASAIHDVDHPGVSNQFLINTNSELALMYNDSSVLENHHLAVGFKLLQEENCDIFQNLTKKQRQSLRKMVIDIVLATDMSKHMNLLADLKTMVETKKGVLLLDNYSDRIQVLQNMVHCADLSNPTKPLQLYRQWTDRIMEEFFRQGDRERERGMEISPMCDKHNASVEKSQVGFIDYIVHPLWETWADLVHPDAQDILDTLEDNREWYQSTIP 411
                                   100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290||     304       314       324       334       344       354       364       374       384       394       404       
                                                                                                                                                                                                                                  291|                                                                                                                   
                                                                                                                                                                                                                                   296                                                                                                                   

   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  (0, 0)

(no "SCOP Domain" information available for 4W1O)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4W1O)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4W1O)

(-) Gene Ontology  (52, 52)

Asymmetric/Biological Unit(hide GO term definitions)

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    His A:389 - Pro A:390   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        PDE4D_HUMAN | Q084991e9k 1mkd 1oyn 1ptw 1q9m 1tb7 1tbb 1xom 1xon 1xoq 1xor 1y2b 1y2c 1y2d 1y2e 1y2k 1zkn 2fm0 2fm5 2pw3 2qyn 3g4g 3g4i 3g4k 3g4l 3g58 3iad 3iak 3k4s 3sl3 3sl4 3sl5 3sl6 3sl8 3v9b 4ogb 4wcu 5k1i 5k32 5tkb 5wqa

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4W1O)