› 5uoy

X-ray diffraction
1.82Å resolution

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)

Released:
DOI: 10.2210/pdb5uoy/pdb
PDB entry 5uoy coloured by chain, front view.
PDB entry 5uoy coloured by chain, side view.
PDB entry 5uoy coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Discovery of Selective Phosphodiesterase 1 Inhibitors with Memory Enhancing Properties.
Dyck B, Branstetter B, Gharbaoui T, Hudson AR, Breitenbucher JG, Gomez L, Botrous I, Marrone T, Barido R, Allerston CK, Cedervall EP, Xu R, Sridhar V, Barker R, Aertgeerts K, Schmelzer K, Neul D, Lee D, Massari ME, Andersen CB, Sebring K, Zhou X, Petroski R, Limberis J, Augustin M, Chun LE, Edwards TE, Peters M, Tabatabaei A
J Med Chem 60 3472-3483 (2017)
PMID: 28406621

Function and Biology Details

Reaction catalysed: 
Nucleoside 3',5'-cyclic phosphate + H(2)O = nucleoside 5'-phosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-169511 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Dual specificity calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B Chain: A
Molecule details ›
Chain: A
Length: 361 amino acids
Theoretical weight: 41.28 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q01064 (Residues: 146-506; Coverage: 67%)
Gene names: PDE1B, PDES1B
Sequence domains: 3'5'-cyclic nucleotide phosphodiesterase
Structure domains: 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain

Ligands and Environments

3 bound ligands:
Ligand ZN 1 x ZN
Ligand MG 1 x MG
Ligand 8HM 2 x 8HM
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.2
Spacegroup: P43212
Unit cell:
a: 87.507Å b: 87.507Å c: 134.714Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.191 0.189 0.221
Expression system: Escherichia coli

Quick links

Citations

5 review citations

Therapeutic targeting of 3',5'-cyclic nucleotide phosphodiesterases: inhibition and beyond.
Baillie et al. (2019)
4 more