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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN PDE1B CATALYTIC DOMAIN IN COMPLEX WITH INHIBITOR 16J (6-(4-METHOXYBENZYL)-9-((TETRAHYDRO-2H-PYRAN-4-YL) 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)
 
Authors :  E. P. Cedervall, C. K. Allerston, R. Xu, V. Sridhar, R. Barker, K. Aertge
Date :  01 Feb 17  (Deposition) - 26 Apr 17  (Release) - 10 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.82
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Hydrolase Inhibitor, 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 - CALCIUM/CALMODULIN-DEPENDENT 3',5'-CYCLIC NUCLEOTIDE PHOSPHODIESTERASE 1B
    Chains: A
    EC Number: 3.1.4.17
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PDE1B, PDE1B1, PDES1B
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CAM-PDE 1B,63 KDA CAM-PDE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
18HM2Ligand/Ion6-[(4-METHOXYPHENYL)METHYL]-9-[(OXAN-4-YL)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
2MG1Ligand/IonMAGNESIUM ION
3ZN1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:227 , HIS A:263 , ASP A:264 , ASP A:370 , HOH A:712 , HOH A:755binding site for residue ZN A 601
2AC2SOFTWAREASP A:264 , HOH A:712 , HOH A:740 , HOH A:743 , HOH A:746 , HOH A:803binding site for residue MG A 602
3AC3SOFTWARETYR A:222 , HIS A:373 , LEU A:388 , MET A:389 , PHE A:392 , PRO A:408 , LEU A:409 , GLN A:421 , PHE A:424 , HOH A:704binding site for residue 8HM A 603
4AC4SOFTWARETYR A:150 , ARG A:181 , THR A:182 , PHE A:185 , THR A:201 , MET A:205 , PRO A:408 , PHE A:427 , HOH A:721binding site for residue 8HM A 604

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5UOY)

(-) 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    
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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:321
                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh.......hhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhh...hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5uoy A 150 YSTAVLNCLKNLDLWCFDVFSLNQAADDHALRTIVFELLTRHNLISRFKIPTVFLMSFLDALETGYGKYKNPYHNQIHAADVTQTVHCFLLRTGMVHCLSEIELLAIIFAAAIHDYEHTGTTNSFHIQTKSECAIVYNDRSVLENHHISSVFRLMQDDEMNIFINLTKDEFVELRALVIEMVLATDMSCHFQQVKTMKTALQQLERIDKPKALSLLLHAADISHPTKQWLVHSRWTKALMEEFFRQGDKEAELGLPFSPLCDRTSTLVAQSQIGFIDFIVEPTFSVLTDVAEKSVPDVVSFRSTWVKRIQENKQKWKERAA 501
                                   159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439    || 480       490       500 
                                                                                                                                                                                                                                                                                                                                444|                         
                                                                                                                                                                                                                                                                                                                                 476
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  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 5UOY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (27, 27)

Asymmetric/Biological Unit(hide GO term definitions)

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  5uoy
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 Related Entries

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

UniProtKB/Swiss-Prot
        PDE1B_HUMAN | Q01064: 1lxr 1taz 4npv 4npw 5b25 5up0

(-) Related Entries Specified in the PDB File

5up0