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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN PHOSPHODIESTERASE 4D IN COMPLEX WITH A TETRAFLUORANLINE COMPOUND
 
Authors :  J. S. Sack
Date :  06 Oct 16  (Deposition) - 28 Dec 16  (Release) - 28 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.16
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Phosphodiesterase, Pde4D, Alternative Splicing, Camp, Cytoplasm, Cytoskeleton, Hydrolase, Membrane, Metal- Binding, Phosphoprotein, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Moslin, D. Gardner, J. Santella, Y. Zhang, J. V. Duncia, C. Liu, J. Lin, J. S. Tokarski, J. Strnad, J. Pedicord, J. Chen, Y. Blat, A. Zupa-Fernandez, L. Cheng, H. Sun, C. Chaudhry, C. Huang, C. D'Arienzo, J. S. Sack, J. K. Muckelbauer, C. Chang, J. Tredup, D. Xie N. Aranibar, J. R. Burke, P. H. Carter, D. S. Weinstein
Identification Of Imidazo[1, 2-B]Pyridazine Tyk2 Pseudokinas Ligands As Potent And Selective Allosteric Inhibitors Of Tyk2 Signalling
Medchemcomm 2016
PubMed: search  |  Reference-DOI: 10.1039/C6MD00560H

(-) Compounds

Molecule 1 - CAMP-SPECIFIC 3',5'-CYCLIC PHOSPHODIESTERASE 4D
    Chains: A, B, C, D
    EC Number: 3.1.4.53
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Plasmid: PBACGUS
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Fragment: UNP RESIDUES 380-753
    Gene: PDE4D, DPDE3
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DPDE3,PDE43

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 23)

Asymmetric Unit (5, 23)
No.NameCountTypeFull Name
17DJ4Ligand/IonN-[(2R)-2,3-DIHYDROXY-2-METHYLPROPYL]-8-(METHYLAMINO)-6-[(2,3,5,6-TETRAFLUOROPHENYL)AMINO]IMIDAZO[1,2-B]PYRIDAZINE-3-CARBOXAMIDE
2EOH8Ligand/IonETHANOL
3MG4Ligand/IonMAGNESIUM ION
4SO43Ligand/IonSULFATE ION
5ZN4Ligand/IonZINC ION
Biological Unit 1 (3, 5)
No.NameCountTypeFull Name
17DJ1Ligand/IonN-[(2R)-2,3-DIHYDROXY-2-METHYLPROPYL]-8-(METHYLAMINO)-6-[(2,3,5,6-TETRAFLUOROPHENYL)AMINO]IMIDAZO[1,2-B]PYRIDAZINE-3-CARBOXAMIDE
2EOH3Ligand/IonETHANOL
3MG-1Ligand/IonMAGNESIUM ION
4SO41Ligand/IonSULFATE ION
5ZN-1Ligand/IonZINC ION
Biological Unit 2 (3, 5)
No.NameCountTypeFull Name
17DJ1Ligand/IonN-[(2R)-2,3-DIHYDROXY-2-METHYLPROPYL]-8-(METHYLAMINO)-6-[(2,3,5,6-TETRAFLUOROPHENYL)AMINO]IMIDAZO[1,2-B]PYRIDAZINE-3-CARBOXAMIDE
2EOH3Ligand/IonETHANOL
3MG-1Ligand/IonMAGNESIUM ION
4SO41Ligand/IonSULFATE ION
5ZN-1Ligand/IonZINC ION
Biological Unit 3 (3, 3)
No.NameCountTypeFull Name
17DJ1Ligand/IonN-[(2R)-2,3-DIHYDROXY-2-METHYLPROPYL]-8-(METHYLAMINO)-6-[(2,3,5,6-TETRAFLUOROPHENYL)AMINO]IMIDAZO[1,2-B]PYRIDAZINE-3-CARBOXAMIDE
2EOH1Ligand/IonETHANOL
3MG-1Ligand/IonMAGNESIUM ION
4SO41Ligand/IonSULFATE ION
5ZN-1Ligand/IonZINC ION
Biological Unit 4 (2, 2)
No.NameCountTypeFull Name
17DJ1Ligand/IonN-[(2R)-2,3-DIHYDROXY-2-METHYLPROPYL]-8-(METHYLAMINO)-6-[(2,3,5,6-TETRAFLUOROPHENYL)AMINO]IMIDAZO[1,2-B]PYRIDAZINE-3-CARBOXAMIDE
2EOH1Ligand/IonETHANOL
3MG-1Ligand/IonMAGNESIUM ION
4SO4-1Ligand/IonSULFATE ION
5ZN-1Ligand/IonZINC ION

(-) Sites  (23, 23)

Asymmetric Unit (23, 23)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:330 , HIS A:366 , ASP A:367 , ASP A:484 , HOH A:901 , HOH A:974binding site for residue ZN A 801
02AC2SOFTWAREASP A:367 , HOH A:901 , HOH A:902 , HOH A:955 , HOH A:963 , HOH A:987binding site for residue MG A 802
03AC3SOFTWAREHIS A:271 , VAL A:272 , PHE A:273 , ARG A:274 , LEU A:494 , GLN A:497binding site for residue SO4 A 803
04AC4SOFTWARELYS A:428 , ASP A:432 , HOH B:818binding site for residue EOH A 804
05AC5SOFTWARETHR A:314 , HIS A:318 , GLU A:409 , PHE C:377 , THR C:381binding site for residue EOH A 805
06AC6SOFTWAREPHE A:404 , ARG A:423 , HOH A:972binding site for residue EOH A 806
07AC7SOFTWAREHIS A:326 , THR A:437 , MET A:439 , ASP A:484 , LEU A:485 , ASN A:487 , ILE A:502 , MET A:523 , GLN A:535 , PHE A:538 , HOH A:919 , HOH A:1024binding site for residue 7DJ A 807
08AC8SOFTWAREHIS B:330 , HIS B:366 , ASP B:367 , ASP B:484 , HOH B:812 , HOH B:854binding site for residue ZN B 701
09AC9SOFTWAREASP B:367 , HOH B:812 , HOH B:814 , HOH B:816 , HOH B:826 , HOH B:856binding site for residue MG B 702
10AD1SOFTWAREHIS B:271 , VAL B:272 , PHE B:273 , ARG B:274 , GLN B:493 , LEU B:494 , GLN B:497binding site for residue SO4 B 703
11AD2SOFTWAREPRO B:522binding site for residue EOH B 704
12AD3SOFTWAREHIS B:318 , GLU B:409 , HOH B:830 , THR D:381binding site for residue EOH B 705
13AD4SOFTWAREHOH A:915 , LYS B:428 , ASP B:432binding site for residue EOH B 706
14AD5SOFTWARETHR B:437 , MET B:439 , ASP B:484 , LEU B:485 , ASN B:487 , ILE B:502 , MET B:523 , GLN B:535 , PHE B:538 , HOH B:806binding site for residue 7DJ B 707
15AD6SOFTWAREHIS C:330 , HIS C:366 , ASP C:367 , ASP C:484 , HOH C:814 , HOH C:868binding site for residue ZN C 701
16AD7SOFTWAREASP C:367 , HOH C:814 , HOH C:820 , HOH C:826 , HOH C:842 , HOH C:871binding site for residue MG C 702
17AD8SOFTWAREHIS C:271 , VAL C:272 , PHE C:273 , ARG C:274 , GLN C:493 , LEU C:494 , GLN C:497binding site for residue SO4 C 703
18AD9SOFTWARELYS C:428 , ASP C:432 , HOH D:831binding site for residue EOH C 704
19AE1SOFTWARETHR C:437 , MET C:439 , ASP C:484 , LEU C:485 , ASN C:487 , ILE C:502 , PHE C:506 , MET C:523 , GLN C:535 , PHE C:538 , HOH C:801binding site for residue 7DJ C 705
20AE2SOFTWAREHIS D:330 , HIS D:366 , ASP D:367 , ASP D:484 , HOH D:801 , HOH D:867binding site for residue ZN D 701
21AE3SOFTWAREASP D:367 , HOH D:801 , HOH D:806 , HOH D:835 , HOH D:849 , HOH D:891binding site for residue MG D 702
22AE4SOFTWAREHOH C:822 , LYS D:428 , ASP D:432binding site for residue EOH D 703
23AE5SOFTWARETHR D:437 , MET D:439 , ASP D:484 , LEU D:485 , ASN D:487 , ILE D:502 , PHE D:506 , MET D:523 , GLN D:535 , PHE D:538 , HOH D:805 , HOH D:941binding site for residue 7DJ D 704

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5TKB)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1His A:555 -Pro A:556
2His B:555 -Pro B:556
3His C:555 -Pro C:556
4His D:555 -Pro D:556

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5TKB)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5TKB)

(-) Exons   (0, 0)

(no "Exon" information available for 5TKB)

(-) Sequences/Alignments

Asymmetric 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:326
                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh.....hhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhh...hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5tkb A 250 VKTEQEDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQERDLLKTFKIPVDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPALEAVFTDLEILAAIFASAIHDVDHPGVSNQFLINTNSELALMYNDSSVLENHHLAVGFKLLQEENCDIFQNLTKKQRQSLRKMVIDIVLATDMSKHMNLLADLKTMVETKKVTVLLLDNYSDRIQVLQNMVHCADLSNPTKPLQLYRQWTDRIMEEFFRQGDRERERGMEISPMCDKHNASVEKSQVGFIDYIVHPLWETWADLVHPDAQDILDTLEDNREWYQSTIPQ 578
                                   259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459|      472       482       492       502       512       522       532       542       552       562       572      
                                                                                                                                                                                                                                           459|                                                                                                                   
                                                                                                                                                                                                                                            463                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:323
                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh.......hhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhh...hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5tkb B 253 EQEDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQERDLLKTFKIPVDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPALEAVFTDLEILAAIFASAIHDVDHPGVSNQFLINTNSELALMYNDSSVLENHHLAVGFKLLQEENCDIFQNLTKKQRQSLRKMVIDIVLATDMSKHMNLLADLKTMVTKVTSGVLLLDNYSDRIQVLQNMVHCADLSNPTKPLQLYRQWTDRIMEEFFRQGDRERERGMEISPMCDKHNASVEKSQVGFIDYIVHPLWETWADLVHPDAQDILDTLEDNREWYQSTIPQ 578
                                   262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452|||||| 465       475       485       495       505       515       525       535       545       555       565       575   
                                                                                                                                                                                                                                  453|||||                                                                                                                     
                                                                                                                                                                                                                                   455||||                                                                                                                     
                                                                                                                                                                                                                                    456|||                                                                                                                     
                                                                                                                                                                                                                                     458||                                                                                                                     
                                                                                                                                                                                                                                      459|                                                                                                                     
                                                                                                                                                                                                                                       461                                                                                                                     


Chain C from PDB  Type:PROTEIN  Length:323
                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh.......hhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhh...hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5tkb C 252 TEQEDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQERDLLKTFKIPVDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPALEAVFTDLEILAAIFASAIHDVDHPGVSNQFLINTNSELALMYNDSSVLENHHLAVGFKLLQEENCDIFQNLTKKQRQSLRKMVIDIVLATDMSKHMNLLADLKTMVETKKVVLLLDNYSDRIQVLQNMVHCADLSNPTKPLQLYRQWTDRIMEEFFRQGDRERERGMEISPMCDKHNASVEKSQVGFIDYIVHPLWETWADLVHPDAQDILDTLEDNREWYQSTIPQ 578
                                   261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451      |465       475       485       495       505       515       525       535       545       555       565       575   
                                                                                                                                                                                                                                        458|                                                                                                                   
                                                                                                                                                                                                                                         463                                                                                                                   


Chain D from PDB  Type:PROTEIN  Length:325
                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh.....hhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhh...hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5tkb D 254 QEDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQERDLLKTFKIPVDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPALEAVFTDLEILAAIFASAIHDVDHPGVSNQFLINTNSELALMYNDSSVLENHHLAVGFKLLQEENCDIFQNLTKKQRQSLRKMVIDIVLATDMSKHMNLLADLKTMVETKKVTSSGVLLLDNYSDRIQVLQNMVHCADLSNPTKPLQLYRQWTDRIMEEFFRQGDRERERGMEISPMCDKHNASVEKSQVGFIDYIVHPLWETWADLVHPDAQDILDTLEDNREWYQSTIPQ 578
                                   263       273       283       293       303       313       323       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
   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)

(no "SCOP Domain" information available for 5TKB)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5TKB)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5TKB)

(-) Gene Ontology  (52, 52)

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  PDE4D_HUMAN | Q08499
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 Related Entries

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

UniProtKB/Swiss-Prot
        PDE4D_HUMAN | Q08499: 1e9k 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 4w1o 4wcu 5k1i 5k32 5wqa

(-) Related Entries Specified in the PDB File

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