› 6cyb

X-ray diffraction
1.62Å resolution

PDE2 in complex with compound 7

Released:
DOI: 10.2210/pdb6cyb/pdb
PDB entry 6cyb coloured by chain, front view.
PDB entry 6cyb coloured by chain, side view.
PDB entry 6cyb coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure-Guided Design and Procognitive Assessment of a Potent and Selective Phosphodiesterase 2A Inhibitor.
Stachel SJ, Berger R, Nomland AB, Ginnetti AT, Paone DV, Wang D, Puri V, Lange H, Drott J, Lu J, Marcus J, Dwyer MP, Suon S, Uslaner JM, Smith SM
ACS Med Chem Lett 9 815-820 (2018)
PMID: 30128073

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:
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
Molecule details ›
Chains: A, B
Length: 373 amino acids
Theoretical weight: 43.69 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: O00408 (Residues: 578-919; Coverage: 36%)
Gene name: PDE2A
Sequence domains: 3'5'-cyclic nucleotide phosphodiesterase
Structure domains: 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain

Ligands and Environments

4 bound ligands:
Ligand ZN 2 x ZN
Ligand MG 2 x MG
Ligand EDO 8 x EDO
Ligand FKV 2 x FKV
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 17-ID
Spacegroup: P212121
Unit cell:
a: 72.26Å b: 96.64Å c: 102.04Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.18 0.179 0.201
Expression system: Spodoptera frugiperda

Quick links

Citations

2 citation in other articles

Chemical Space Exploration with Active Learning and Alchemical Free Energies.
Khalak et al. (2022)
1 more