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(-) Description

Title :  CRYSTAL STRUCTURE OF PDE10A IN COMPLEX WITH ASP9436
 
Authors :  Y. Amano, K. Honbou
Date :  02 Feb 15  (Deposition) - 17 Jun 15  (Release) - 24 Jun 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.03
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Phosphodiesterase, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Hamaguchi, N. Masuda, S. Miyamoto, S. Kikuchi, F. Narazaki, Y. Shiina, R. Seo, Y. Amano, T. Mihara, H. Moriguchi, K. Hattori
Addressing Phototoxicity Observed In A Novel Series Of Biaryl Derivatives: Discovery Of Potent, Selective And Orally Active Phosphodiesterase 10A Inhibitor Asp9436
Bioorg. Med. Chem. V. 23 3351 2015
PubMed-ID: 25960322  |  Reference-DOI: 10.1016/J.BMC.2015.04.052

(-) Compounds

Molecule 1 - CAMP AND CAMP-INHIBITED CGMP 3',5'-CYCLIC PHOSPHODIESTERASE 10A
    Chains: A, B
    EC Number: 3.1.4.17, 3.1.4.35
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 439-779
    Gene: PDE10A
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
14901Ligand/Ion1-METHYL-5-(1-METHYL-3-{[4-(1-METHYL-1H-BENZIMIDAZOL-4-YL)PHENOXY]METHYL}-1H-PYRAZOL-4-YL)PYRIDIN-2(1H)-ONE
2MG2Ligand/IonMAGNESIUM ION
3ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
14901Ligand/Ion1-METHYL-5-(1-METHYL-3-{[4-(1-METHYL-1H-BENZIMIDAZOL-4-YL)PHENOXY]METHYL}-1H-PYRAZOL-4-YL)PYRIDIN-2(1H)-ONE
2MG-1Ligand/IonMAGNESIUM ION
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1490-1Ligand/Ion1-METHYL-5-(1-METHYL-3-{[4-(1-METHYL-1H-BENZIMIDAZOL-4-YL)PHENOXY]METHYL}-1H-PYRAZOL-4-YL)PYRIDIN-2(1H)-ONE
2MG-1Ligand/IonMAGNESIUM ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:529 , HIS A:563 , ASP A:564 , ASP A:674 , HOH A:922 , HOH A:928binding site for residue ZN A 801
2AC2SOFTWAREASP A:564 , HOH A:923 , HOH A:924 , HOH A:926 , HOH A:928 , HOH A:960binding site for residue MG A 802
3AC3SOFTWARETYR A:524 , LEU A:635 , SER A:677 , ILE A:692 , TYR A:693 , PHE A:696 , PRO A:712 , MET A:713 , GLY A:725 , GLN A:726 , PHE A:729binding site for residue 490 A 803
4AC4SOFTWAREHIS B:529 , HIS B:563 , ASP B:564 , ASP B:674 , MG B:802 , HOH B:923 , HOH B:924binding site for residue ZN B 801
5AC5SOFTWAREASP B:564 , ZN B:801 , HOH B:918 , HOH B:920 , HOH B:921 , HOH B:922 , HOH B:923binding site for residue MG B 802

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4XY2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4XY2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4XY2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4XY2)

(-) Exons   (0, 0)

(no "Exon" information available for 4XY2)

(-) 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:312
                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhh...hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4xy2 A 447 HMSICTSEEWQGLMQFTLPVRLCKEIELFHFDIGPFENMWPGIFVYMVHRSCGTSCFELEKLCRFIMSVKKNYRRVPYHNWKHAVTVAHCMYAILQNNHTLFTDLERKGLLIACLCHDLDHRGFSNSYSTSTMEQHHFSQTVSILQLEGHNIFSTLSSSEYEQVLEIIRKAIIATDLALYFGNRKQLEEMYQTGSLNLNNQSHRDRVIGLMMTACDLCSVTKLWPVTKLTANDIYAEFWAEGDEMKKLGIQPIPMMDRDKKDEVPQGQLGFYNAVAIPCYTTLTQILPPTEPLLKACRDNLSQWEKVIRGEE 770
                                   456       466       476       486       496       506       516       526       536       546       556       566       588       598       608       618       628       638       648       658       668       678       688       698       708       718       728       738       748       758       768  
                                                                                                                                                         574|                                                                                                                                                                                       
                                                                                                                                                          587                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:322
                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhh..hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhh.hhhhh..hhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xy2 B 447 HMSICTSEEWQGLMQFTLPVRLCKEIELFHFDIGPFENMWPGIFVYMVHRSCGTSCFELEKLCRFIMSVKKNYRRVPYHNWKHAVTVAHCMYAILQNNHTLFTDLERKGLLIACLCHDLDHRGFSNSYLQKFPLAALYSTSTMEQHHFSQTVSILQLEGHNIFSTLSSSEYEQVLEIIRKAIIATDLALYFGNRKQLEEMYQTGSLNLNNQSHRDRVIGLMMTACDLCSVTKLWPVTKLTANDIYAEFWAEGDEMKKLGIQPIPMMDRDKKDEVPQGQLGFYNAVAIPCYTTLTQILPPTEPLLKACRDNLSQWEKVIRGEE 770
                                   456       466       476       486       496       506       516       526       536       546       556       566       576 ||    588       598       608       618       628       638       648       658       668       678       688       698       708       718       728       738       748       758       768  
                                                                                                                                                             578|                                                                                                                                                                                             
                                                                                                                                                              581
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 4XY2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4XY2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4XY2)

(-) Gene Ontology  (24, 24)

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  4xy2
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 Related Entries

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

UniProtKB/Swiss-Prot
        PDE10_HUMAN | Q9Y233: 1lrb 2oun 2oup 2ouq 2our 2ous 2ouu 2ouv 2ouy 2wey 2y0j 2zmf 3sn7 3sni 3snl 3ui7 3uuo 3wi2 3ws8 3ws9 3wyk 3wyl 3wym 4ael 4ajd 4ajf 4ajg 4ajm 4bbx 4ddl 4dff 4fcb 4fcd 4heu 4hf4 4lkq 4llj 4llk 4llp 4llx 4lm0 4lm1 4lm2 4lm3 4lm4 4mrw 4mrz 4ms0 4msa 4msc 4mse 4msh 4msn 4muw 4mvh 4p0n 4p1r 4phw 4tpm 4tpp 4wn1 4yqh 4ys7 4zo5 5axp 5axq 5b4k 5b4l 5c1w 5c28 5c29 5c2a 5c2e 5c2h 5dh4 5dh5 5ede 5edg 5edh 5edi 5i2r 5k9r 5uwf

(-) Related Entries Specified in the PDB File

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