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› 6zqz

X-ray diffraction
1.88Å resolution

[1,2,4]Triazolo[1,5-a]pyrimidine Phosphodiesterase 2 Inhibitors

Released:
DOI: 10.2210/pdb6zqz/pdb
Model geometry
Fit model/data
PDB entry 6zqz coloured by chain, front view.
PDB entry 6zqz coloured by chain, side view.
PDB entry 6zqz coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
[1,2,4]Triazolo[1,5-a]pyrimidine Phosphodiesterase 2A Inhibitors: Structure and Free-Energy Perturbation-Guided Exploration.
Tresadern G, Velter I, Trabanco AA, Van den Keybus F, Macdonald GJ, Somers MVF, Vanhoof G, Leonard PM, Lamers MBAC, Van Roosbroeck YEM, Buijnsters PJJA
J Med Chem 63 12887-12910 (2020)
PMID: 33105987

Function and Biology Details

Reaction catalysed: 
[a nucleoside 3',5'-cyclic phosphate + H2O = a nucleoside 5'-phosphate +H(+)., a nucleoside 3',5'-cyclic phosphate + H2O = a nucleoside 5'-phosphate +H(+)., a nucleoside 3',5'-cyclic phosphate + H2O = a nucleoside 5'-phosphate +H(+)., a nucleoside 3',5'-cyclic phosphate + H2O = a nucleoside 5'-phosphate +H(+).]
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-126261 (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: 353 amino acids
Theoretical weight: 41.43 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: O00408 (Residues: 578-921; Coverage: 37%)
Gene name: PDE2A
Sequence domains: 3'5'-cyclic nucleotide phosphodiesterase

Ligands and Environments

3 bound ligands:
Ligand ZN 4 x ZN
Ligand MG 5 x MG
Ligand QOQ 4 x QOQ
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: DIAMOND BEAMLINE I02
Spacegroup: P1
Unit cell:
a: 55.96Å b: 73.46Å c: 92.23Å
α: 109.16° β: 91.37° γ: 91.26°
R-values:
R R work R free
0.199 0.196 0.244
Expression system: Spodoptera frugiperda

Quick links

Citations

3 citation in other articles

The maximal and current accuracy of rigorous protein-ligand binding free energy calculations.
Ross et al. (2023)
2 more