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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PDE9A CATALYTIC DOMAIN IN COMPLEX WITH INHIBITOR 28
 
Authors :  J. Hou, H. Ke
Date :  07 Aug 12  (Deposition) - 03 Oct 12  (Release) - 14 Nov 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Pde9A, , Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Meng, J. Hou, Y. X. Shao, P. Y. Wu, M. Huang, X. Zhu, Y. Cai, Z. Li, J. Xu, P. Liu, H. B. Luo, Y. Wan, H. Ke
Structure-Based Discovery Of Highly Selective Phosphodiesterase-9A Inhibitors And Implications For Inhibitor Design.
J. Med. Chem. V. 55 8549 2012
PubMed-ID: 22985069  |  Reference-DOI: 10.1021/JM301189C

(-) Compounds

Molecule 1 - HIGH AFFINITY CGMP-SPECIFIC 3',5'-CYCLIC PHOSPHODIESTERASE 9A
    Chains: A, B
    EC Number: 3.1.4.35
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(CODONPLUS)
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 241-566
    Gene: PDE9A
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1LUO3Ligand/IonN-(4-METHOXYPHENYL)-N~2~-[1-(2-METHYLPHENYL)-4-OXO-4,5-DIHYDRO-1H-PYRAZOLO[3,4-D]PYRIMIDIN-6-YL]-L-ALANINAMIDE
2MG2Ligand/IonMAGNESIUM ION
3ZN2Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:365 , LEU A:420 , TYR A:424 , ALA A:452 , GLN A:453 , PHE A:456BINDING SITE FOR RESIDUE LUO A 601
2AC2SOFTWAREHIS A:256 , HIS A:292 , ASP A:293 , ASP A:402 , HOH A:701 , HOH A:702BINDING SITE FOR RESIDUE ZN A 602
3AC3SOFTWAREASP A:293 , HOH A:702 , HOH A:703 , HOH A:704 , HOH A:705 , HOH A:706BINDING SITE FOR RESIDUE MG A 603
4AC4SOFTWAREALA A:499 , MET A:500 , LEU A:503 , MET B:365 , LEU B:420 , TYR B:424 , ALA B:452 , GLN B:453 , PHE B:456 , LUO B:602BINDING SITE FOR RESIDUE LUO B 601
5AC5SOFTWAREARG A:495 , ALA A:499 , PHE B:441 , THR B:451 , ALA B:452 , ILE B:454 , GLY B:455 , LUO B:601BINDING SITE FOR RESIDUE LUO B 602
6AC6SOFTWAREHIS B:256 , HIS B:292 , ASP B:293 , ASP B:402 , HOH B:701 , HOH B:702BINDING SITE FOR RESIDUE ZN B 603
7AC7SOFTWAREASP B:293 , HIS B:325 , HOH B:701 , HOH B:703 , HOH B:704 , HOH B:705 , HOH B:706BINDING SITE FOR RESIDUE MG B 604

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4GH6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4GH6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4GH6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4GH6)

(-) Exons   (0, 0)

(no "Exon" information available for 4GH6)

(-) 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:326
                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains d4gh6a_ A: High-affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A, PDE9A                                                                                                                                                                                                                                                        SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhh...hhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh....hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gh6 A 181 PTYPKYLLSPETIEALRKPTFDVWLWEPNEMLSCLEHMYHDLGLVRDFSINPVTLRRWLFCVHDNYRNNPFHNFRHCFCVAQMMYSMVWLCSLQEKFSQTDILILMTAAICHDLDHPGYNNTYQINARTELAVRYNDISPLENHHCAVAFQILAEPECNIFSNIPPDGFKQIRQGMITLILATDMARHAEIMDSFKEKMENFDYSNEEHMTLLKMILIKCCDISNEVRPMEVAEPWVDCLLEEYFMQSDREKSEGLPVAPFMDRDKVTKATAQIGFIKFVLIPMFETVTKLFPMVEEIMLQPLWESRDRYEELKRIDDAMKELQKK 506
                                   190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500      


Chain B from PDB  Type:PROTEIN  Length:326
                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains d4gh6b_ B: High-affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A, PDE9A                                                                                                                                                                                                                                                        SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhh...hhhhhhhhhhhhhhh.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh....hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gh6 B 181 PTYPKYLLSPETIEALRKPTFDVWLWEPNEMLSCLEHMYHDLGLVRDFSINPVTLRRWLFCVHDNYRNNPFHNFRHCFCVAQMMYSMVWLCSLQEKFSQTDILILMTAAICHDLDHPGYNNTYQINARTELAVRYNDISPLENHHCAVAFQILAEPECNIFSNIPPDGFKQIRQGMITLILATDMARHAEIMDSFKEKMENFDYSNEEHMTLLKMILIKCCDISNEVRPMEVAEPWVDCLLEEYFMQSDREKSEGLPVAPFMDRDKVTKATAQIGFIKFVLIPMFETVTKLFPMVEEIMLQPLWESRDRYEELKRIDDAMKELQKK 506
                                   190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4GH6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4GH6)

(-) Gene Ontology  (22, 22)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        PDE9A_HUMAN | O76083: 2hd1 2yy2 3dy8 3dyl 3dyn 3dyq 3dys 3jsi 3jsw 3k3e 3k3h 3n3z 3qi3 3qi4 4e90 4g2j 4g2l 4y86 4y87 4y8c

(-) Related Entries Specified in the PDB File

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