› 5u00

X-ray diffraction
1.41Å resolution

CRYSTAL STRUCTURE OF HUMAN PHOSPHODIESTERASE 2A IN COMPLEX WITH 3,3-difluoro-1-[(4-fluoro-3-iodophenyl)carbonyl]-5-{5-methyl-[1,2,4]triazolo[1,5-a]pyrimidin-7-yl}piperidine

Released:
DOI: 10.2210/pdb5u00/pdb
PDB entry 5u00 coloured by chain, front view.
PDB entry 5u00 coloured by chain, side view.
PDB entry 5u00 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Design and Synthesis of Novel and Selective Phosphodiesterase 2 (PDE2a) Inhibitors for the Treatment of Memory Disorders.
Gomez L, Massari ME, Vickers T, Freestone G, Vernier W, Ly K, Xu R, McCarrick M, Marrone T, Metz M, Yan YG, Yoder ZW, Lemus R, Broadbent NJ, Barido R, Warren N, Schmelzer K, Neul D, Lee D, Andersen CB, Sebring K, Aertgeerts K, Zhou X, Tabatabaei A, Peters M, Breitenbucher JG
J Med Chem 60 2037-2051 (2017)
PMID: 28165743

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-126260 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
cGMP-dependent 3',5'-cyclic phosphodiesterase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 344 amino acids
Theoretical weight: 40.17 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: O00408 (Residues: 579-919; Coverage: 36%)
Gene name: PDE2A
Sequence domains: 3'5'-cyclic nucleotide phosphodiesterase
Structure domains: 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain

Ligands and Environments

3 bound ligands:
Ligand 7OV 4 x 7OV
Ligand ZN 4 x ZN
Ligand MG 4 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.2
Spacegroup: P1
Unit cell:
a: 55.986Å b: 73.249Å c: 91.206Å
α: 109.38° β: 90.79° γ: 91.1°
R-values:
R R work R free
0.201 0.199 0.228
Expression system: Trichoplusia ni

Quick links

Citations

1 review citation

1,2,4-Triazolo[1,5-a]pyrimidines in drug design.
Oukoloff et al. (2019)
7 other articles

1 mention without citation

A systematic analysis of atomic protein-ligand interactions in the PDB.
Ferreira de Freitas et al. (2017)