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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN PDE10A IN COMPLEX WITH INHIBITOR 16D
 
Authors :  R. Xu, E. P. Cedervall, V. Sridhar, R. Barker, K. Aertgeerts
Date :  21 Feb 17  (Deposition) - 26 Apr 17  (Release) - 10 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.87
Chains :  Asym. Unit :  C,D
Biol. Unit 1:  C  (1x)
Biol. Unit 2:  D  (1x)
Keywords :  Phosphodiesterase, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Dyck, B. Branstetter, T. Gharbaoui, A. R. Hudson, J. G. Breitenbucher, L. Gomez, I. Botrous, T. Marrone, R. Barido, C. K. Allerston, E. P. Cedervall, R. Xu, V. Sridhar, R. Barker, K. Aertgeerts, K. Schmelzer, D. Neul, D. Lee, M. E. Massari, C. B. Andersen, K. Sebring, X. Zhou, R. Petroski, J. Limberis, M. Augustin, L. E. Chun, T. E. Edwards, M. Peters, A. Tabatabaei
Discovery Of Selective Phosphodiesterase 1 Inhibitors With Memory Enhancing Properties.
J. Med. Chem. V. 60 3472 2017
PubMed-ID: 28406621  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.7B00302

(-) Compounds

Molecule 1 - CAMP AND CAMP-INHIBITED CGMP 3',5'-CYCLIC PHOSPHODIESTERASE 10A
    Chains: C, D
    EC Number: 3.1.4.17, 3.1.4.35
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: ROSETTA(DE3)
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 449-789
    Gene: PDE10A
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : CD
Biological Unit 1 (1x): C 
Biological Unit 2 (1x):  D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
18Q72Ligand/Ion9-[(1S)-2,2-DIFLUOROCYCLOPROPANE-1-CARBONYL]-6-[(4-METHOXYPHENYL)METHYL]-8,9,10,11-TETRAHYDROPYRIDO[4',3':4,5]THIENO[3,2-E][1,2,4]TRIAZOLO[1,5-C]PYRIMIDIN-5(6H)-ONE
2MG2Ligand/IonMAGNESIUM ION
3ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
18Q71Ligand/Ion9-[(1S)-2,2-DIFLUOROCYCLOPROPANE-1-CARBONYL]-6-[(4-METHOXYPHENYL)METHYL]-8,9,10,11-TETRAHYDROPYRIDO[4',3':4,5]THIENO[3,2-E][1,2,4]TRIAZOLO[1,5-C]PYRIMIDIN-5(6H)-ONE
2MG-1Ligand/IonMAGNESIUM ION
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
18Q71Ligand/Ion9-[(1S)-2,2-DIFLUOROCYCLOPROPANE-1-CARBONYL]-6-[(4-METHOXYPHENYL)METHYL]-8,9,10,11-TETRAHYDROPYRIDO[4',3':4,5]THIENO[3,2-E][1,2,4]TRIAZOLO[1,5-C]PYRIMIDIN-5(6H)-ONE
2MG-1Ligand/IonMAGNESIUM ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR C:524 , HIS C:525 , LEU C:675 , SER C:677 , VAL C:678 , ILE C:692 , TYR C:693 , PHE C:696 , ILE C:711 , MET C:713 , GLN C:726 , PHE C:729 , HOH C:914 , HOH C:1051 , LYS D:705 , LEU D:706 , GLY D:707 , HOH D:1109binding site for residue 8Q7 C 801
2AC2SOFTWAREHIS C:529 , HIS C:563 , ASP C:564 , ASP C:674 , MG C:803 , HOH C:984 , HOH C:1025binding site for residue ZN C 802
3AC3SOFTWAREASP C:564 , ZN C:802 , HOH C:915 , HOH C:917 , HOH C:984 , HOH C:989 , HOH C:993binding site for residue MG C 803
4AC4SOFTWARETYR D:524 , HIS D:525 , LEU D:675 , SER D:677 , VAL D:678 , ILE D:692 , TYR D:693 , PHE D:696 , MET D:713 , GLN D:726 , PHE D:729 , VAL D:733 , HOH D:919 , HOH D:969binding site for residue 8Q7 D 801
5AC5SOFTWAREHIS D:529 , HIS D:563 , ASP D:564 , ASP D:674 , HOH D:907binding site for residue ZN D 802
6AC6SOFTWAREASP D:564 , HOH D:901 , HOH D:907 , HOH D:909 , HOH D:946 , HOH D:1008binding site for residue MG D 803

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5UWF)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5UWF)

(-) 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 C from PDB  Type:PROTEIN  Length:323
                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhh....hhhhhhh......hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhh..hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5uwf C 446 SMASICTSEEWQGLMQFTLPVRLCKEIELFHFDIGPFENMWPGIFVYMVHRSCGTSCFELEKLCRFIMSVKKNYRRVPYHNWKHAVTVAHCMYAILQNNHTLFTDLERKGLLIACLCHDLDHRGFSNSYLQKFDHPLAALYSTSTMEQHHFSQTVSILQLEGHNIFSTLSSSEYEQVLEIIRKAIIATDLALYFGNRKQLEEMYQTGSLNLNNQSHRDRVIGLMMTACDLCSVTKLWPVTKLTANDIYAEFWAEGDEMKKLGIQPIPMMDRDKKDEVPQGQLGFYNAVAIPCYTTLTQILPPTEPLLKACRDNLSQWEKVIRG 768
                                   455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765   


Chain D from PDB  Type:PROTEIN  Length:324
                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhhhhhhh...hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhh..hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5uwf D 446 SMASICTSEEWQGLMQFTLPVRLCKEIELFHFDIGPFENMWPGIFVYMVHRSCGTSCFELEKLCRFIMSVKKNYRRVPYHNWKHAVTVAHCMYAILQNNHTLFTDLERKGLLIACLCHDLDHRGFSNSYLQKFDHPLAALYSTSTMEQHHFSQTVSILQLEGHNIFSTLSSSEYEQVLEIIRKAIIATDLALYFGNRKQLEEMYQTGSLNLNNQSHRDRVIGLMMTACDLCSVTKLWPVTKLTANDIYAEFWAEGDEMKKLGIQPIPMMDRDKKDEVPQGQLGFYNAVAIPCYTTLTQILPPTEPLLKACRDNLSQWEKVIRGE 769
                                   455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765
   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 5UWF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (24, 24)

Asymmetric Unit(hide GO term definitions)

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        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 4xy2 4yqh 4ys7 4zo5 5axp 5axq 5b4k 5b4l 5c1w 5c28 5c29 5c2a 5c2e 5c2h 5dh4 5dh5 5ede 5edg 5edh 5edi 5i2r 5k9r

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