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(-) Description

Title :  PDE2A CATALYTIC DOMAIN IN COMPLEX WITH A BRAIN PENETRANT INHIBITOR
 
Authors :  P. Buijnsters, J. I. Andres, M. Deangelis, X. Langlois, F. Rombouts, W. Sanderson, G. Tresadern, A. Trabanco, G. Vanhoof, Y. Vanroosbroec
Date :  24 Apr 14  (Deposition) - 06 Aug 14  (Release) - 24 Sep 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
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 :  Hydrolase, Binding Sites, Catalytic Domain, Cyclic Nucleotide Phosphodiesterases, Type 2, Type 4, Disease Models, Animal, Drug Evaluation, Preclinical, Phosphodiesterase 2 Inhibitors, Phosphodiesterase Inhibitors, Protein Binding, Structure-Activity Relationship (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. Buijnsters, M. De Angelis, X. Langlois, F. J. R. Rombouts, W. Sanderson, G. Tresadern, A. Ritchie, A. A. Trabanco, G. Vanhoof, Y. V. Roosbroeck, J. Andres
Structure-Based Design Of A Potent, Selective, And Brain Penetrating Pde2 Inhibitor With Demonstrated Target Engagement.
Acs Med. Chem. Lett. V. 5 1049 2014
PubMed-ID: 25221665  |  Reference-DOI: 10.1021/ML500262U

(-) Compounds

Molecule 1 - CGMP-DEPENDENT 3', 5'-CYCLIC PHOSPHODIESTERASE
    ChainsA, B, C, D
    EC Number3.1.4.17
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System CommonFALL ARMYWORM
    Expression System Taxid7108
    Expression System Vector TypeBACULOVIRUS
    FragmentCATALYTIC DOMAIN, RESDIUES 579-921
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCYCLIC GMP-STIMULATED PHOSPHODIESTERASE, CGS-PDE, CGSPDE, PDE2A

 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
1MG4Ligand/IonMAGNESIUM ION
2Q2T4Ligand/Ion1-(5-BUTOXYPYRIDIN-3-YL)-4-METHYL-8-(MORPHOLIN-4-YLMETHYL)[1,2,4]TRIAZOLO[4,3-A]QUINOXALINE
3ZN4Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2Q2T1Ligand/Ion1-(5-BUTOXYPYRIDIN-3-YL)-4-METHYL-8-(MORPHOLIN-4-YLMETHYL)[1,2,4]TRIAZOLO[4,3-A]QUINOXALINE
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2Q2T1Ligand/Ion1-(5-BUTOXYPYRIDIN-3-YL)-4-METHYL-8-(MORPHOLIN-4-YLMETHYL)[1,2,4]TRIAZOLO[4,3-A]QUINOXALINE
3ZN-1Ligand/IonZINC ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2Q2T1Ligand/Ion1-(5-BUTOXYPYRIDIN-3-YL)-4-METHYL-8-(MORPHOLIN-4-YLMETHYL)[1,2,4]TRIAZOLO[4,3-A]QUINOXALINE
3ZN-1Ligand/IonZINC ION
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2Q2T1Ligand/Ion1-(5-BUTOXYPYRIDIN-3-YL)-4-METHYL-8-(MORPHOLIN-4-YLMETHYL)[1,2,4]TRIAZOLO[4,3-A]QUINOXALINE
3ZN-1Ligand/IonZINC ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:660 , HIS A:696 , ASP A:697 , ASP A:808 , HOH A:2062 , HOH A:2076BINDING SITE FOR RESIDUE ZN A1001
02AC2SOFTWAREASN A:704 , THR A:768 , ASP A:808 , GLN A:812 , PHE A:830 , MET A:848 , GLN A:859 , PHE A:862 , HOH A:2061 , HOH A:2134 , HOH A:2173BINDING SITE FOR RESIDUE Q2T A1918
03AC3SOFTWAREASP A:697 , HOH A:2063 , HOH A:2075 , HOH A:2076 , HOH A:2077 , HOH A:2095BINDING SITE FOR RESIDUE MG A1919
04AC4SOFTWAREHIS B:660 , HIS B:696 , ASP B:697 , ASP B:808 , HOH B:2049 , HOH B:2061BINDING SITE FOR RESIDUE ZN B1001
05AC5SOFTWAREASN B:704 , THR B:768 , ASP B:808 , GLN B:812 , ILE B:826 , PHE B:830 , GLN B:859 , PHE B:862 , HOH B:2046 , HOH B:2104 , HOH B:2124 , HOH B:2131 , HOH B:2168BINDING SITE FOR RESIDUE Q2T B1917
06AC6SOFTWAREASP B:697 , HOH B:2048 , HOH B:2060 , HOH B:2061 , HOH B:2062 , HOH B:2076BINDING SITE FOR RESIDUE MG B1918
07AC7SOFTWAREHIS C:660 , HIS C:696 , ASP C:697 , ASP C:808 , HOH C:2032 , HOH C:2038BINDING SITE FOR RESIDUE ZN C1001
08AC8SOFTWAREHIS C:656 , THR C:768 , ASP C:808 , GLN C:812 , PHE C:830 , MET C:845 , MET C:848 , GLN C:859 , PHE C:862 , HOH C:2030 , HOH C:2078 , HOH C:2091 , HOH C:2129BINDING SITE FOR RESIDUE Q2T C1917
09AC9SOFTWAREASP C:697 , HOH C:2031 , HOH C:2037 , HOH C:2038 , HOH C:2039 , HOH C:2061BINDING SITE FOR RESIDUE MG C1918
10BC1SOFTWAREHIS D:660 , HIS D:696 , ASP D:697 , ASP D:808 , HOH D:2031 , HOH D:2042BINDING SITE FOR RESIDUE ZN D1001
11BC2SOFTWAREASN D:704 , THR D:768 , ASP D:808 , GLN D:812 , ILE D:826 , MET D:845 , MET D:848 , GLN D:859 , PHE D:862 , HOH D:2029 , HOH D:2083 , HOH D:2111 , HOH D:2158BINDING SITE FOR RESIDUE Q2T D1922
12BC3SOFTWAREASP D:697 , HOH D:2030 , HOH D:2041 , HOH D:2042 , HOH D:2043 , HOH D:2066BINDING SITE FOR RESIDUE MG D1923

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4D08)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4D08)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4D08)

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDEASE_IPS00126 3'5'-cyclic nucleotide phosphodiesterases signature.PDE2A_HUMAN696-707
 
 
 
  4A:696-707
B:696-707
C:696-707
D:696-707
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDEASE_IPS00126 3'5'-cyclic nucleotide phosphodiesterases signature.PDE2A_HUMAN696-707
 
 
 
  1A:696-707
-
-
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDEASE_IPS00126 3'5'-cyclic nucleotide phosphodiesterases signature.PDE2A_HUMAN696-707
 
 
 
  1-
B:696-707
-
-
Biological Unit 3 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDEASE_IPS00126 3'5'-cyclic nucleotide phosphodiesterases signature.PDE2A_HUMAN696-707
 
 
 
  1-
-
C:696-707
-
Biological Unit 4 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDEASE_IPS00126 3'5'-cyclic nucleotide phosphodiesterases signature.PDE2A_HUMAN696-707
 
 
 
  1-
-
-
D:696-707

(-) Exons   (11, 44)

Asymmetric Unit (11, 44)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003344561bENSE00001920521chr11:72385463-72385181283PDE2A_HUMAN1-24240--
1.8dENST000003344568dENSE00001337724chr11:72353370-7235329873PDE2A_HUMAN24-48250--
1.10ENST0000033445610ENSE00001337723chr11:72319795-7231970690PDE2A_HUMAN49-78300--
1.11ENST0000033445611ENSE00001337722chr11:72316270-7231618289PDE2A_HUMAN79-108300--
1.13ENST0000033445613ENSE00001337720chr11:72308663-72308554110PDE2A_HUMAN108-145380--
1.14aENST0000033445614aENSE00001337719chr11:72307692-7230763756PDE2A_HUMAN145-163190--
1.15aENST0000033445615aENSE00001337718chr11:72302400-7230234160PDE2A_HUMAN164-183200--
1.16ENST0000033445616ENSE00001337717chr11:72301624-72301471154PDE2A_HUMAN184-235520--
1.17bENST0000033445617bENSE00001337716chr11:72301288-7230123653PDE2A_HUMAN235-252180--
1.18ENST0000033445618ENSE00001337715chr11:72301025-7230095175PDE2A_HUMAN253-277250--
1.19ENST0000033445619ENSE00001337714chr11:72300836-7230079542PDE2A_HUMAN278-291140--
1.20ENST0000033445620ENSE00001337713chr11:72300284-7230021966PDE2A_HUMAN292-313220--
1.21ENST0000033445621ENSE00001337712chr11:72299958-72299828131PDE2A_HUMAN314-357440--
1.22ENST0000033445622ENSE00001337711chr11:72297225-72297114112PDE2A_HUMAN357-394380--
1.23ENST0000033445623ENSE00001337710chr11:72296637-7229659840PDE2A_HUMAN395-408140--
1.24ENST0000033445624ENSE00001337709chr11:72296478-7229641564PDE2A_HUMAN408-429220--
1.25ENST0000033445625ENSE00001337707chr11:72295988-7229591673PDE2A_HUMAN429-453250--
1.26bENST0000033445626bENSE00001337705chr11:72295772-72295595178PDE2A_HUMAN454-513600--
1.27bENST0000033445627bENSE00001337704chr11:72295357-72295245113PDE2A_HUMAN513-550380--
1.28ENST0000033445628ENSE00001337703chr11:72294559-7229448278PDE2A_HUMAN551-576260--
1.29ENST0000033445629ENSE00001337702chr11:72293610-72293488123PDE2A_HUMAN577-617414A:579-617
B:580-617
C:590-617
D:584-617 (gaps)
39
38
28
34
1.30bENST0000033445630bENSE00001337701chr11:72292991-7229292171PDE2A_HUMAN618-641244A:618-641
B:618-641
C:618-641
D:618-641
24
24
24
24
1.31ENST0000033445631ENSE00001337700chr11:72292523-72292401123PDE2A_HUMAN641-682424A:641-682
B:641-682
C:641-682
D:641-682
42
42
42
42
1.32ENST0000033445632ENSE00001337698chr11:72292017-7229193088PDE2A_HUMAN682-711304A:682-711
B:682-711
C:682-711
D:682-711
30
30
30
30
1.33ENST0000033445633ENSE00001337697chr11:72291668-7229162148PDE2A_HUMAN712-727164A:712-727
B:712-727
C:712-727
D:712-727
16
16
16
16
1.34ENST0000033445634ENSE00001337695chr11:72290652-7229057875PDE2A_HUMAN728-752254A:728-752
B:728-752
C:728-752
D:728-752
25
25
25
25
1.35aENST0000033445635aENSE00001337694chr11:72290427-72290328100PDE2A_HUMAN753-786344A:753-786
B:753-786
C:753-786
D:753-786
34
34
34
34
1.36bENST0000033445636bENSE00001337693chr11:72290053-72289941113PDE2A_HUMAN786-823384A:786-823
B:786-823
C:786-823
D:786-823
38
38
38
38
1.37ENST0000033445637ENSE00001337692chr11:72289558-7228952039PDE2A_HUMAN824-836134A:824-836
B:824-836
C:824-836
D:824-836
13
13
13
13
1.38ENST0000033445638ENSE00001337689chr11:72289383-72289277107PDE2A_HUMAN837-872364A:837-872
B:837-872
C:837-872
D:837-872
36
36
36
36
1.40bENST0000033445640bENSE00001836179chr11:72288638-722871851454PDE2A_HUMAN872-941704A:872-917
B:872-916
C:872-916
D:872-921
46
45
45
50

(-) 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:339
 aligned with PDE2A_HUMAN | O00408 from UniProtKB/Swiss-Prot  Length:941

    Alignment length:339
                                   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         
          PDE2A_HUMAN   579 DDEYTKLLHDGIQPVAAIDSNFASFTYTPRSLPEDDTSMAILSMLQDMNFINNYKIDCPTLARFCLMVKKGYRDPPYHNWMHAFSVSHFCYLLYKNLELTNYLEDIEIFALFISCMCHDLDHRGTNNSFQVASKSVLAALYSSEGSVMERHHFAQAIAILNTHGCNIFDHFSRKDYQRMLDLMRDIILATDLAHHLRIFKDLQKMAEVGYDRNNKQHHRLLLCLLMTSCDLSDQTKGWKTTRKIAELIYKEFFSQGDLEKAMGNRPMEMMDREKAYIPELQISFMEHIAMPIYKLLQDLFPKAAELYERVASNREHWTKVSHKFTIRGLPSNNSLDFLD 917
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh...hhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhhh...hhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.........hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------PDEASE_I    ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.29  PDB: A:579-617 [INCOMPLETE] Exon 1.30b              ----------------------------------------Exon 1.32  PDB: A:682-711     Exon 1.33       Exon 1.34  PDB: A:728-752Exon 1.35a  PDB: A:753-786        -------------------------------------Exon 1.37    Exon 1.38  PDB: A:837-872           --------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------Exon 1.31  PDB: A:641-682 UniProt: 641-682-------------------------------------------------------------------------------------------------------Exon 1.36b  PDB: A:786-823            ------------------------------------------------Exon 1.40b  PDB: A:872-917 UniProt: 872-941    Transcript 1 (2)
                 4d08 A 579 DDEYTKLLHDGIQPVAAIDSNFASFTYTPRSLPEDDTSMAILSMLQDMNFINNYKIDCPTLARFCLMVKKGYRDPPYHNWMHAFSVSHFCYLLYKNLELTNYLEDIEIFALFISCMCHDLDHRGTNNSFQVASKSVLAALYSSEGSVMERHHFAQAIAILNTHGCNIFDHFSRKDYQRMLDLMRDIILATDLAHHLRIFKDLQKMAEVGYDRNNKQHHRLLLCLLMTSCDLSDQTKGWKTTRKIAELIYKEFFSQGDLEKAMGNRPMEMMDREKAYIPELQISFMEHIAMPIYKLLQDLFPKAAELYERVASNREHWTKVSHKFTIRGLPSNNSLDFLD 917
                                   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:337
 aligned with PDE2A_HUMAN | O00408 from UniProtKB/Swiss-Prot  Length:941

    Alignment length:337
                                   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       
          PDE2A_HUMAN   580 DEYTKLLHDGIQPVAAIDSNFASFTYTPRSLPEDDTSMAILSMLQDMNFINNYKIDCPTLARFCLMVKKGYRDPPYHNWMHAFSVSHFCYLLYKNLELTNYLEDIEIFALFISCMCHDLDHRGTNNSFQVASKSVLAALYSSEGSVMERHHFAQAIAILNTHGCNIFDHFSRKDYQRMLDLMRDIILATDLAHHLRIFKDLQKMAEVGYDRNNKQHHRLLLCLLMTSCDLSDQTKGWKTTRKIAELIYKEFFSQGDLEKAMGNRPMEMMDREKAYIPELQISFMEHIAMPIYKLLQDLFPKAAELYERVASNREHWTKVSHKFTIRGLPSNNSLDFL 916
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh...hhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhh....hhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------PDEASE_I    ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.29  PDB: B:580-617 [INCOMPLETE]Exon 1.30b              ----------------------------------------Exon 1.32  PDB: B:682-711     Exon 1.33       Exon 1.34  PDB: B:728-752Exon 1.35a  PDB: B:753-786        -------------------------------------Exon 1.37    Exon 1.38  PDB: B:837-872           -------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------Exon 1.31  PDB: B:641-682 UniProt: 641-682-------------------------------------------------------------------------------------------------------Exon 1.36b  PDB: B:786-823            ------------------------------------------------Exon 1.40b  PDB: B:872-916 UniProt: 872-941   Transcript 1 (2)
                 4d08 B 580 DEYTKLLHDGIQPVAAIDSNFASFTYTPRSLPEDDTSMAILSMLQDMNFINNYKIDCPTLARFCLMVKKGYRDPPYHNWMHAFSVSHFCYLLYKNLELTNYLEDIEIFALFISCMCHDLDHRGTNNSFQVASKSVLAALYSSEGSVMERHHFAQAIAILNTHGCNIFDHFSRKDYQRMLDLMRDIILATDLAHHLRIFKDLQKMAEVGYDRNNKQHHRLLLCLLMTSCDLSDQTKGWKTTRKIAELIYKEFFSQGDLEKAMGNRPMEMMDREKAYIPELQISFMEHIAMPIYKLLQDLFPKAAELYERVASNREHWTKVSHKFTIRGLPSNNSLDFL 916
                                   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
 aligned with PDE2A_HUMAN | O00408 from UniProtKB/Swiss-Prot  Length:941

    Alignment length:327
                                   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       
          PDE2A_HUMAN   590 IQPVAAIDSNFASFTYTPRSLPEDDTSMAILSMLQDMNFINNYKIDCPTLARFCLMVKKGYRDPPYHNWMHAFSVSHFCYLLYKNLELTNYLEDIEIFALFISCMCHDLDHRGTNNSFQVASKSVLAALYSSEGSVMERHHFAQAIAILNTHGCNIFDHFSRKDYQRMLDLMRDIILATDLAHHLRIFKDLQKMAEVGYDRNNKQHHRLLLCLLMTSCDLSDQTKGWKTTRKIAELIYKEFFSQGDLEKAMGNRPMEMMDREKAYIPELQISFMEHIAMPIYKLLQDLFPKAAELYERVASNREHWTKVSHKFTIRGLPSNNSLDFL 916
               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 ----------------------------------------------------------------------------------------------------------PDEASE_I    ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.29  PDB: C:590-617   Exon 1.30b              ----------------------------------------Exon 1.32  PDB: C:682-711     Exon 1.33       Exon 1.34  PDB: C:728-752Exon 1.35a  PDB: C:753-786        -------------------------------------Exon 1.37    Exon 1.38  PDB: C:837-872           -------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------Exon 1.31  PDB: C:641-682 UniProt: 641-682-------------------------------------------------------------------------------------------------------Exon 1.36b  PDB: C:786-823            ------------------------------------------------Exon 1.40b  PDB: C:872-916 UniProt: 872-941   Transcript 1 (2)
                 4d08 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:335
 aligned with PDE2A_HUMAN | O00408 from UniProtKB/Swiss-Prot  Length:941

    Alignment length:338
                                   593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803       813       823       833       843       853       863       873       883       893       903       913        
          PDE2A_HUMAN   584 KLLHDGIQPVAAIDSNFASFTYTPRSLPEDDTSMAILSMLQDMNFINNYKIDCPTLARFCLMVKKGYRDPPYHNWMHAFSVSHFCYLLYKNLELTNYLEDIEIFALFISCMCHDLDHRGTNNSFQVASKSVLAALYSSEGSVMERHHFAQAIAILNTHGCNIFDHFSRKDYQRMLDLMRDIILATDLAHHLRIFKDLQKMAEVGYDRNNKQHHRLLLCLLMTSCDLSDQTKGWKTTRKIAELIYKEFFSQGDLEKAMGNRPMEMMDREKAYIPELQISFMEHIAMPIYKLLQDLFPKAAELYERVASNREHWTKVSHKFTIRGLPSNNSLDFLDEEYE 921
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...---..hhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhhh...hhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------PDEASE_I    ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.29  PDB: D:584-617 (gaps)  Exon 1.30b              ----------------------------------------Exon 1.32  PDB: D:682-711     Exon 1.33       Exon 1.34  PDB: D:728-752Exon 1.35a  PDB: D:753-786        -------------------------------------Exon 1.37    Exon 1.38  PDB: D:837-872           ------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------Exon 1.31  PDB: D:641-682 UniProt: 641-682-------------------------------------------------------------------------------------------------------Exon 1.36b  PDB: D:786-823            ------------------------------------------------Exon 1.40b  PDB: D:872-921 UniProt: 872-941        Transcript 1 (2)
                 4d08 D 584 KLL---IQPVAAIDSNFASFTYTPRSLPEDDTSMAILSMLQDMNFINNYKIDCPTLARFCLMVKKGYRDPPYHNWMHAFSVSHFCYLLYKNLELTNYLEDIEIFALFISCMCHDLDHRGTNNSFQVASKSVLAALYSSEGSVMERHHFAQAIAILNTHGCNIFDHFSRKDYQRMLDLMRDIILATDLAHHLRIFKDLQKMAEVGYDRNNKQHHRLLLCLLMTSCDLSDQTKGWKTTRKIAELIYKEFFSQGDLEKAMGNRPMEMMDREKAYIPELQISFMEHIAMPIYKLLQDLFPKAAELYERVASNREHWTKVSHKFTIRGLPSNNSLDFLDEEYE 921
                              |   |593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803       813       823       833       843       853       863       873       883       893       903       913        
                            586 590                                                                                                                                                                                                                                                                                                                                           

   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 4D08)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4D08)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4D08)

(-) Gene Ontology  (50, 50)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (PDE2A_HUMAN | O00408)
molecular function
    GO:0004115    3',5'-cyclic-AMP phosphodiesterase activity    Catalysis of the reaction: adenosine 3',5'-cyclic phosphate + H2O = adenosine 5'-phosphate.
    GO:0047555    3',5'-cyclic-GMP phosphodiesterase activity    Catalysis of the reaction: guanosine 3',5'-cyclic phosphate + H2O = guanosine 5'-phosphate.
    GO:0004114    3',5'-cyclic-nucleotide phosphodiesterase activity    Catalysis of the reaction: nucleoside 3',5'-cyclic phosphate + H2O = nucleoside 5'-phosphate.
    GO:0030911    TPR domain binding    Interacting selectively and non-covalently with a tetratricopeptide repeat (TPR) domain of a protein, the consensus sequence of which is defined by a pattern of small and large hydrophobic amino acids and a structure composed of helices.
    GO:0030552    cAMP binding    Interacting selectively and non-covalently with cAMP, the nucleotide cyclic AMP (adenosine 3',5'-cyclophosphate).
    GO:0030553    cGMP binding    Interacting selectively and non-covalently with cGMP, the nucleotide cyclic GMP (guanosine 3',5'-cyclophosphate).
    GO:0004118    cGMP-stimulated cyclic-nucleotide phosphodiesterase activity    Catalysis of the reaction: nucleoside 3',5'-cyclic phosphate + H2O = nucleoside 5'-phosphate; catalytic activity is increased in the presence of cGMP.
    GO:0005262    calcium channel activity    Enables the facilitated diffusion of a calcium ion (by an energy-independent process) involving passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism.
    GO:0004112    cyclic-nucleotide phosphodiesterase activity    Catalysis of the reaction: a nucleoside cyclic phosphate + H2O = a nucleoside phosphate.
    GO:0008144    drug binding    Interacting selectively and non-covalently with a drug, any naturally occurring or synthetic substance, other than a nutrient, that, when administered or applied to an organism, affects the structure or functioning of the organism; in particular, any such substance used in the diagnosis, prevention, or treatment of disease.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0008081    phosphoric diester hydrolase activity    Catalysis of the hydrolysis of a phosphodiester to give a phosphomonoester and a free hydroxyl group.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
    GO:0006198    cAMP catabolic process    The chemical reactions and pathways resulting in the breakdown of the nucleotide cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate).
    GO:0019933    cAMP-mediated signaling    Any intracellular signal transduction in which the signal is passed on within the cell via cyclic AMP (cAMP). Includes production of cAMP, and downstream effectors that further transmit the signal within the cell.
    GO:0046069    cGMP catabolic process    The chemical reactions and pathways resulting in the breakdown of cyclic GMP, guanosine 3',5'-phosphate.
    GO:0019934    cGMP-mediated signaling    Any intracellular signal transduction in which the signal is passed on within the cell via cyclic GMP (cGMP). Includes production of cGMP, and downstream effectors that further transmit the signal within the cell.
    GO:0070588    calcium ion transmembrane transport    A process in which a calcium ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
    GO:0071321    cellular response to cGMP    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cGMP (cyclic GMP, guanosine 3',5'-cyclophosphate) stimulus.
    GO:0035690    cellular response to drug    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    GO:0097011    cellular response to granulocyte macrophage colony-stimulating factor stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a granulocyte macrophage colony-stimulating factor stimulus.
    GO:0036006    cellular response to macrophage colony-stimulating factor stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a macrophage colony-stimulating factor stimulus.
    GO:0071260    cellular response to mechanical stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a mechanical stimulus.
    GO:0071560    cellular response to transforming growth factor beta stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a transforming growth factor beta stimulus.
    GO:0061028    establishment of endothelial barrier    The establishment of a barrier between endothelial cell layers, such as those in the brain, lung or intestine, to exert specific and selective control over the passage of water and solutes, thus allowing formation and maintenance of compartments that differ in fluid and solute composition.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0030224    monocyte differentiation    The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of a monocyte.
    GO:0030818    negative regulation of cAMP biosynthetic process    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of the nucleotide cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate).
    GO:0033159    negative regulation of protein import into nucleus, translocation    Any process that stops, prevents or reduces the vectorial transfer of a protein from the cytoplasm into the nucleus, across the nuclear membrane.
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0043116    negative regulation of vascular permeability    Any process that reduces the extent to which blood vessels can be pervaded by fluid.
    GO:0050729    positive regulation of inflammatory response    Any process that activates or increases the frequency, rate or extent of the inflammatory response.
    GO:0043117    positive regulation of vascular permeability    Any process that increases the extent to which blood vessels can be pervaded by fluid.
    GO:0006626    protein targeting to mitochondrion    The process of directing proteins towards and into the mitochondrion, usually mediated by mitochondrial proteins that recognize signals contained within the imported protein.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0045121    membrane raft    Any of the small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes. Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions.
    GO:0005759    mitochondrial matrix    The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0042734    presynaptic membrane    A specialized area of membrane of the axon terminal that faces the plasma membrane of the neuron or muscle fiber with which the axon terminal establishes a synaptic junction; many synaptic junctions exhibit structural presynaptic characteristics, such as conical, electron-dense internal protrusions, that distinguish it from the remainder of the axon plasma membrane.

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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 4d09 4htx 4htz 4jib 5tz3 5tza 5tzc 5tzh 5tzw 5tzx 5tzz 5u00 5u7d 5u7i 5u7j 5u7k 5u7l

(-) Related Entries Specified in the PDB File

4d09 PDE2A CATALYTIC DOMAIN IN COMPLEX WITH A BRAIN PENETRANT INHIBITOR