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(-) Description

Title :  PDE2 CATALYTIC DOMAIN COMPLEXED WITH INHIBITORS
 
Authors :  J. Pandit
Date :  12 Dec 16  (Deposition) - 28 Jun 17  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
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 :  Pde2, Sbdd, Inhibitor, Phosphodiesterase, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. J. Helal, E. P. Arnold, T. L. Boyden, C. Chang, T. A. Chappie, K. F. Fennell, M. D. Forman, M. Hajos, J. F. Harms, W. E. Hoffmann, J. M. Humphrey, Z. Kang, R. J. Kleiman, B. L. Kormos, C. W. Lee, J. Lu, N. Maklad, L. Mcdowell, S. Mente, R. E. O'Connor, J. Pandit, M. Piotrowski, A. W. Schmidt, C. J. Schmidt, H. Ueno, P. R. Verhoest, E. X. Yang
Application Of Structure-Based Design And Parallel Chemistr To Identify A Potent, Selective, And Brain Penetrant Phosphodiesterase 2A Inhibitor.
J. Med. Chem. 2017
PubMed-ID: 28574706  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.7B00397

(-) Compounds

Molecule 1 - CGMP-DEPENDENT 3',5'-CYCLIC PHOSPHODIESTERASE
    ChainsA, B, C, D
    EC Number3.1.4.17
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System StrainSF21
    Expression System Taxid7108
    FragmentCATALYTIC DOMAIN OF PDE2, UNP RESIDUES 323-663
    GenePDE2A
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCYCLIC GMP-STIMULATED PHOSPHODIESTERASE,CGSPDE

 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  (3, 12)

Asymmetric Unit (3, 12)
No.NameCountTypeFull Name
17XS4Ligand/Ion4-[3-(4-METHOXYPHENOXY)AZETIDIN-1-YL]-1-METHYL-3-(2-METHYLPROPYL)-1H-PYRAZOLO[3,4-D]PYRIMIDINE
2MG4Ligand/IonMAGNESIUM ION
3ZN4Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
17XS1Ligand/Ion4-[3-(4-METHOXYPHENOXY)AZETIDIN-1-YL]-1-METHYL-3-(2-METHYLPROPYL)-1H-PYRAZOLO[3,4-D]PYRIMIDINE
2MG-1Ligand/IonMAGNESIUM ION
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
17XS1Ligand/Ion4-[3-(4-METHOXYPHENOXY)AZETIDIN-1-YL]-1-METHYL-3-(2-METHYLPROPYL)-1H-PYRAZOLO[3,4-D]PYRIMIDINE
2MG-1Ligand/IonMAGNESIUM ION
3ZN-1Ligand/IonZINC ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
17XS1Ligand/Ion4-[3-(4-METHOXYPHENOXY)AZETIDIN-1-YL]-1-METHYL-3-(2-METHYLPROPYL)-1H-PYRAZOLO[3,4-D]PYRIMIDINE
2MG-1Ligand/IonMAGNESIUM ION
3ZN-1Ligand/IonZINC ION
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
17XS1Ligand/Ion4-[3-(4-METHOXYPHENOXY)AZETIDIN-1-YL]-1-METHYL-3-(2-METHYLPROPYL)-1H-PYRAZOLO[3,4-D]PYRIMIDINE
2MG-1Ligand/IonMAGNESIUM ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:655 , HIS A:656 , LEU A:774 , LEU A:809 , GLN A:812 , ILE A:826 , GLN A:859 , PHE A:862 , ILE A:866 , HOH A:1113 , HOH A:1241binding site for residue 7XS A 1001
02AC2SOFTWAREHIS A:660 , HIS A:696 , ASP A:697 , ASP A:808 , HOH A:1129 , HOH A:1197binding site for residue ZN A 1002
03AC3SOFTWAREASP A:697 , HOH A:1102 , HOH A:1129 , HOH A:1179 , HOH A:1188 , HOH A:1237binding site for residue MG A 1003
04AC4SOFTWARETYR B:655 , LEU B:809 , GLN B:812 , ILE B:826 , GLN B:859 , PHE B:862 , ILE B:866 , HOH B:1175binding site for residue 7XS B 1001
05AC5SOFTWAREHIS B:660 , HIS B:696 , ASP B:697 , ASP B:808 , HOH B:1101 , HOH B:1201binding site for residue ZN B 1002
06AC6SOFTWAREASP B:697 , HOH B:1101 , HOH B:1103 , HOH B:1114 , HOH B:1165 , HOH B:1206binding site for residue MG B 1003
07AC7SOFTWAREGLY B:589 , TYR C:655 , HIS C:656 , LEU C:809 , GLN C:812 , ILE C:826 , PHE C:830 , GLN C:859 , PHE C:862 , ILE C:866 , HOH C:1182binding site for residue 7XS C 1001
08AC8SOFTWAREHIS C:660 , HIS C:696 , ASP C:697 , ASP C:808 , HOH C:1104 , HOH C:1235binding site for residue ZN C 1002
09AC9SOFTWAREASP C:697 , HOH C:1102 , HOH C:1104 , HOH C:1146 , HOH C:1216 , HOH C:1245binding site for residue MG C 1003
10AD1SOFTWAREGLN A:591 , TYR D:655 , LEU D:774 , LEU D:809 , GLN D:812 , ILE D:826 , GLN D:859 , PHE D:862 , HOH D:1173binding site for residue 7XS D 1001
11AD2SOFTWAREHIS D:660 , HIS D:696 , ASP D:697 , ASP D:808 , HOH D:1150 , HOH D:1190binding site for residue ZN D 1002
12AD3SOFTWAREASP D:697 , HOH D:1104 , HOH D:1118 , HOH D:1150 , HOH D:1208 , HOH D:1227binding site for residue MG D 1003

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5U7I)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Glu B:722 -Gly B:723

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5U7I)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5U7I)

(-) Exons   (0, 0)

(no "Exon" information available for 5U7I)

(-) 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:338
                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh...hhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhhh...hhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5u7i A 579 DDEYTKLLHDGIQPVAAIDSNFASFTYTPRSLPEDDTSMAILSMLQDMNFINNYKIDCPTLARFCLMVKKGYRDPPYHNWMHAFSVSHFCYLLYKNLELTNYLEDIEIFALFISCMCHDLDHRGTNNSFQVASKSVLAALYSSEGSVMERHHFAQAIAILNTHGCNIFDHFSRKDYQRMLDLMRDIILATDLAHHLRIFKDLQKMAEVGYDRNNKQHHRLLLCLLMTSCDLSDQTKGWKTTRKIAELIYKEFFSQGDLEKAMGNRPMEMMDREKAYIPELQISFMEHIAMPIYKLLQDLFPKAAELYERVASNREHWTKVSHKFTIRGLPSNNSLDFL 916
                                   588       598       608       618       628       638       648       658       668       678       688       698       708       718       728       738       748       758       768       778       788       798       808       818       828       838       848       858       868       878       888       898       908        

Chain B from PDB  Type:PROTEIN  Length:336
                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhh...hhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhh....hhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5u7i B 580 DEYTKLLHDGIQPVAAIDSNFASFTYTPRSLPEDDTSMAILSMLQDMNFINNYKIDCPTLARFCLMVKKGYRDPPYHNWMHAFSVSHFCYLLYKNLELTNYLEDIEIFALFISCMCHDLDHRGTNNSFQVASKSVLAALYSSEGSVMERHHFAQAIAILNTHGCNIFDHFSRKDYQRMLDLMRDIILATDLAHHLRIFKDLQKMAEVGYDRNNKQHHRLLLCLLMTSCDLSDQTKGWKTTRKIAELIYKEFFSQGDLEKAMGNRPMEMMDREKAYIPELQISFMEHIAMPIYKLLQDLFPKAAELYERVASNREHWTKVSHKFTIRGLPSNNSLDF 915
                                   589       599       609       619       629       639       649       659       669       679       689       699       709       719       729       739       749       759       769       779       789       799       809       819       829       839       849       859       869       879       889       899       909      

Chain C from PDB  Type:PROTEIN  Length:327
                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhhh...hhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5u7i C 590 IQPVAAIDSNFASFTYTPRSLPEDDTSMAILSMLQDMNFINNYKIDCPTLARFCLMVKKGYRDPPYHNWMHAFSVSHFCYLLYKNLELTNYLEDIEIFALFISCMCHDLDHRGTNNSFQVASKSVLAALYSSEGSVMERHHFAQAIAILNTHGCNIFDHFSRKDYQRMLDLMRDIILATDLAHHLRIFKDLQKMAEVGYDRNNKQHHRLLLCLLMTSCDLSDQTKGWKTTRKIAELIYKEFFSQGDLEKAMGNRPMEMMDREKAYIPELQISFMEHIAMPIYKLLQDLFPKAAELYERVASNREHWTKVSHKFTIRGLPSNNSLDFL 916
                                   599       609       619       629       639       649       659       669       679       689       699       709       719       729       739       749       759       769       779       789       799       809       819       829       839       849       859       869       879       889       899       909       

Chain D from PDB  Type:PROTEIN  Length:324
                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhhh...hhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5u7i D 590 IQPVAAIDSNFASFTYTPRSLPEDDTSMAILSMLQDMNFINNYKIDCPTLARFCLMVKKGYRDPPYHNWMHAFSVSHFCYLLYKNLELTNYLEDIEIFALFISCMCHDLDHRGTNNSFQVASKSVLAALYSSEGSVMERHHFAQAIAILNTHGCNIFDHFSRKDYQRMLDLMRDIILATDLAHHLRIFKDLQKMAEVGYDRNNKQHHRLLLCLLMTSCDLSDQTKGWKTTRKIAELIYKEFFSQGDLEKAMGNRPMEMMDREKAYIPELQISFMEHIAMPIYKLLQDLFPKAAELYERVASNREHWTKVSHKFTIRGLPSNNSL 913
                                   599       609       619       629       639       649       659       669       679       689       699       709       719       729       739       749       759       769       779       789       799       809       819       829       839       849       859       869       879       889       899       909    

   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 5U7I)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5U7I)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5U7I)

(-) Gene Ontology  (50, 50)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        PDE2A_HUMAN | O004081z1l 3ibj 3itm 3itu 4c1i 4d08 4d09 4htx 4htz 4jib 5tz3 5tza 5tzc 5tzh 5tzw 5tzx 5tzz 5u00 5u7d 5u7j 5u7k 5u7l

(-) Related Entries Specified in the PDB File

5u7d 5u7j 5u7k 5u7l