› 4y87

X-ray diffraction
3.1Å resolution

Crystal structure of phosphodiesterase 9 in complex with (R)-C33 (6-{[(1R)-1-(4-chlorophenyl)ethyl]amino}-1-cyclopentyl-1,5-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one)

Released:
DOI: 10.2210/pdb4y87/pdb
PDB entry 4y87 coloured by chain, front view.
PDB entry 4y87 coloured by chain, side view.
PDB entry 4y87 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural Asymmetry of Phosphodiesterase-9A and a Unique Pocket for Selective Binding of a Potent Enantiomeric Inhibitor.
Huang M, Shao Y, Hou J, Cui W, Liang B, Huang Y, Li Z, Wu Y, Zhu X, Liu P, Wan Y, Ke H, Luo HB
Mol Pharmacol 88 836-45 (2015)
PMID: 26316540

Function and Biology Details

Reaction catalysed: 
Guanosine 3',5'-cyclic phosphate + H(2)O = guanosine 5'-phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-131212 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A Chains: A, B
Molecule details ›
Chains: A, B
Length: 533 amino acids
Theoretical weight: 61.79 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: O76083 (Residues: 1-593; Coverage: 90%)
Gene name: PDE9A
Sequence domains: 3'5'-cyclic nucleotide phosphodiesterase
Structure domains: 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain

Ligands and Environments

3 bound ligands:
Ligand 49E 2 x 49E
Ligand ZN 2 x ZN
Ligand MG 2 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-BM
Spacegroup: P41212
Unit cell:
a: 105.436Å b: 105.436Å c: 270.056Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.207 0.205 0.247
Expression system: Escherichia coli BL21

Quick links

Citations

5 review citations

Biopharmaceuticals from microorganisms: from production to purification.
Jozala et al. (2016)
4 more

1 mention without citation

In silico screening of Andrographis paniculata secondary metabolites as anti-diabetes mellitus through PDE9 inhibition.
Ischak et al. (2023)