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(-) Description

Title :  PDE4D CRYSTAL STRUCTURE IN COMPLEX WITH SMALL MOLECULE INHIBITOR
 
Authors :  V. Segarra, B. Hernandez, R. Roberts, J. Gracia, M. Soler, I. Bonin, J. A
Date :  19 May 16  (Deposition) - 29 Mar 17  (Release) - 29 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.99
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Phosphodiesterases, Inhibitor, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. S. Roberts, S. Sevilla, M. Ferrer, J. Taltavull, B. Hernandez, J. Gracia, V. Segarra, M. D. Lehner, A. Gavalda, M. Andres, J. Cabedo, D. Vilella, E. Calama, C. Carcasona, M. Miralpeix, M. Martinell, J. Aymami
4-Amino-7, 8-Dihydro-1, 6-Naphthyridin-5(6H)-Ones As Inhaled Pde4 Inhibitors: Structural Biology, Structure-Activity Relationships And Binding Kinetics
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - CAMP-SPECIFIC 3',5'-CYCLIC PHOSPHODIESTERASE 4D
    Chains: A, B
    EC Number: 3.1.4.53
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Fragment: UNP RESIDUES 88-411
    Gene: PDE4D, DPDE3
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DPDE3,PDE43

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 38)

Asymmetric/Biological Unit (4, 38)
No.NameCountTypeFull Name
16Q22Ligand/Ion4-[(3-METHOXYPHENYL)AMINO]-2-PHENYL-7,8-DIHYDRO-1,6-NAPHTHYRIDIN-5(6H)-ONE
2EDO32Ligand/Ion1,2-ETHANEDIOL
3MG2Ligand/IonMAGNESIUM ION
4ZN2Ligand/IonZINC ION

(-) Sites  (37, 37)

Asymmetric Unit (37, 37)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:164 , HIS A:200 , ASP A:201 , ASP A:318 , MG A:1002 , HOH A:1154 , HOH A:1214binding site for residue ZN A 1001
02AC2SOFTWAREASP A:201 , ZN A:1001 , HOH A:1141 , HOH A:1169 , HOH A:1200 , HOH A:1214 , HOH A:1218binding site for residue MG A 1002
03AC3SOFTWARETYR A:159 , THR A:271 , MET A:273 , ASP A:318 , ASN A:321 , THR A:333 , GLN A:369 , PHE A:372 , EDO A:1010 , EDO A:1011 , EDO A:1013 , HOH A:1122 , HOH A:1186binding site for residue 6Q2 A 1003
04AC4SOFTWARELYS A:262 , ILE A:265 , ASP A:266 , HOH A:1108 , ASN B:224binding site for residue EDO A 1004
05AC5SOFTWAREASN A:209 , GLN A:210 , HOH A:1107 , HOH A:1133 , HOH A:1162 , HOH A:1182binding site for residue EDO A 1005
06AC6SOFTWAREGLU A:150 , TYR A:153 , ASN A:162 , EDO A:1007 , HOH A:1125 , HOH A:1151 , HOH A:1314 , GLN B:407binding site for residue EDO A 1006
07AC7SOFTWAREASN A:115 , ALA A:155 , ASN A:161 , ASN A:162 , ILE A:163 , EDO A:1006 , HOH A:1151binding site for residue EDO A 1007
08AC8SOFTWAREVAL A:174 , SER A:177 , THR A:178 , ASP A:391 , HOH A:1112binding site for residue EDO A 1008
09AC9SOFTWAREPHE A:238 , ARG A:257 , HOH A:1193binding site for residue EDO A 1009
10AD1SOFTWAREHIS A:204 , GLY A:206 , VAL A:207 , SER A:208 , GLU A:339 , PHE A:340 , GLN A:343 , 6Q2 A:1003 , HOH A:1126 , HOH A:1252binding site for residue EDO A 1010
11AD2SOFTWARESER A:368 , GLY A:371 , PHE A:372 , 6Q2 A:1003binding site for residue EDO A 1011
12AD3SOFTWAREHIS A:154 , ASP A:203 , PRO A:205 , LEU A:219binding site for residue EDO A 1012
13AD4SOFTWAREMET A:273 , 6Q2 A:1003binding site for residue EDO A 1013
14AD5SOFTWAREALA A:183 , VAL A:184 , HOH A:1103 , GLY B:114 , ASN B:115 , ARG B:116binding site for residue EDO A 1014
15AD6SOFTWAREPRO A:179 , ALA A:180 , SER A:295 , GLY A:296 , HIS A:389 , PRO A:390 , ASP A:391binding site for residue EDO A 1015
16AD7SOFTWARELEU A:299 , ARG B:335 , ARG B:342 , HOH B:1113 , HOH B:1221binding site for residue EDO A 1016
17AD8SOFTWAREGLU A:366 , TRP A:405 , TYR A:406 , THR A:409binding site for residue EDO A 1017
18AD9SOFTWAREGLU A:111 , ARG A:335 , HOH A:1240binding site for residue EDO A 1018
19AE1SOFTWARELYS A:275 , HOH A:1188binding site for residue EDO A 1019
20AE2SOFTWAREHIS B:164 , HIS B:200 , ASP B:201 , ASP B:318 , MG B:1002 , HOH B:1150 , HOH B:1186binding site for residue ZN B 1001
21AE3SOFTWAREASP B:201 , ZN B:1001 , HOH B:1147 , HOH B:1150 , HOH B:1162 , HOH B:1178 , HOH B:1238binding site for residue MG B 1002
22AE4SOFTWARETYR B:159 , MET B:273 , ASP B:318 , ASN B:321 , TRP B:332 , THR B:333 , ILE B:336 , PHE B:340 , GLN B:369 , PHE B:372 , EDO B:1012 , EDO B:1013 , HOH B:1128binding site for residue 6Q2 B 1003
23AE5SOFTWAREPRO A:411 , GLU B:366 , TRP B:405 , TYR B:406 , HOH B:1127binding site for residue EDO B 1004
24AE6SOFTWAREPHE B:238 , ARG B:257 , ARG B:261 , EDO B:1006 , HOH B:1119 , HOH B:1196binding site for residue EDO B 1005
25AE7SOFTWAREARG B:257 , GLN B:258 , EDO B:1005 , HOH B:1212binding site for residue EDO B 1006
26AE8SOFTWARELYS B:262 , ASP B:266 , HOH B:1102 , HOH B:1203binding site for residue EDO B 1007
27AE9SOFTWARETRP A:405 , ASP B:401 , ASN B:402binding site for residue EDO B 1008
28AF1SOFTWAREMET B:277 , LYS B:284binding site for residue EDO B 1009
29AF2SOFTWAREASP A:151 , HIS A:152 , GLY B:371 , ASP B:374 , TYR B:375 , HOH B:1138binding site for residue EDO B 1010
30AF3SOFTWAREHIS B:160 , HIS B:204 , GLY B:206 , VAL B:207 , GLU B:339 , PHE B:340 , GLN B:343 , HOH B:1124 , HOH B:1143binding site for residue EDO B 1011
31AF4SOFTWARESER B:368 , GLY B:371 , PHE B:372 , 6Q2 B:1003binding site for residue EDO B 1012
32AF5SOFTWAREMET B:273 , 6Q2 B:1003binding site for residue EDO B 1013
33AF6SOFTWARELYS B:239binding site for residue EDO B 1014
34AF7SOFTWAREHIS B:154 , ASP B:203 , PRO B:205 , LEU B:219binding site for residue EDO B 1015
35AF8SOFTWARETHR B:293 , SER B:294 , VAL B:297 , HOH B:1303binding site for residue EDO B 1016
36AF9SOFTWAREVAL A:297 , LEU A:299 , HOH B:1142binding site for residue EDO B 1018
37AG1SOFTWAREALA B:183 , PHE B:185 , ILE B:190 , HOH B:1116binding site for residue EDO B 1019

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5K32)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1His A:389 -Pro A:390
2Leu B:300 -Asp B:301
3His B:389 -Pro B:390

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5K32)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5K32)

(-) Exons   (0, 0)

(no "Exon" information available for 5K32)

(-) 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 hhhhhhhhhh.......hhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhhh..hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5k32 A  88 QEDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQERDLLKTFKIPVDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPALEAVFTDLEILAAIFASAIHDVDHPGVSNQFLINTNSELALMYNDSSVLENHHLAVGFKLLQEENCDIFQNLTKKQRQSLRKMVIDIVLATDMSKHMNLLADLKTMVETKKVTSSGVLLLDNYSDRIQVLQNMVHCADLSNPTKPLQLYRQWTDRIMEEFFRQGDRERERGMEISCDKHNASVEKSQVGFIDYIVHPLWETWADLVHPDAQDILDTLEDNREWYQSTIP 411
                                    97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       359       369       379       389       399       409  
                                                                                                                                                                                                                                                                                                     355|                                                     
                                                                                                                                                                                                                                                                                                      358                                                     


Chain B from PDB  Type:PROTEIN  Length:321
                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh.......hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhh...hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5k32 B  87 AQEDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQERDLLKTFKIPVDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPALEAVFTDLEILAAIFASAIHDVDHPGVSNQFLINTNSELALMYNDSSVLENHHLAVGFKLLQEENCDIFQNLTKKQRQSLRKMVIDIVLATDMSKHMNLLADLKTMVETKKVTSVLLLDNYSDRIQVLQNMVHCADLSNPTKPLQLYRQWTDRIMEEFFRQGDRERERGMEISCDKHNASVEKSQVGFIDYIVHPLWETWADLVHPDAQDILDTLEDNREWYQSTIP 411
                                    96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       298       308       318       328       338       348      |360       370       380       390       400       410 
                                                                                                                                                                                                                                         294|                                                       355|                                                     
                                                                                                                                                                                                                                          297                                                        358
   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 5K32)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5K32)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5K32)

(-) Gene Ontology  (52, 52)

Asymmetric/Biological Unit(hide GO term definitions)

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    Leu B:300 - Asp B:301   [ RasMol ]  
 

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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 5tkb 5wqa

(-) Related Entries Specified in the PDB File

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