› 7b9h

X-ray diffraction
1.5Å resolution

Crystal structure of the PDE4D catalytic domain in complex with GEBR-42a

Released:
DOI: 10.2210/pdb7b9h/pdb
PDB entry 7b9h coloured by chain, front view.
PDB entry 7b9h coloured by chain, side view.
PDB entry 7b9h coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Design, synthesis, biological evaluation and structural characterization of novel GEBR library PDE4D inhibitors.
Brullo C, Rapetti F, Abbate S, Prosdocimi T, Torretta A, Semrau M, Massa M, Alfei S, Storici P, Parisini E, Bruno O
Eur J Med Chem 223 113638 (2021)
PMID: 34171658

Function and Biology Details

Reaction catalysed: 
Adenosine 3',5'-cyclic phosphate + H(2)O = adenosine 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-170655 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
3',5'-cyclic-AMP phosphodiesterase 4D Chains: A, B
Molecule details ›
Chains: A, B
Length: 343 amino acids
Theoretical weight: 39.62 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q08499 (Residues: 380-714; Coverage: 41%)
Gene names: DPDE3, PDE4D
Sequence domains: 3'5'-cyclic nucleotide phosphodiesterase

Ligands and Environments

4 bound ligands:
Ligand ZN 2 x ZN
Ligand MG 8 x MG
Ligand EDO 28 x EDO
Ligand T3K 2 x T3K
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06DA
Spacegroup: P212121
Unit cell:
a: 64.748Å b: 98.628Å c: 119.821Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.196 0.194 0.221
Expression system: Escherichia coli

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Citations

1 review citation

The Magic Methyl and Its Tricks in Drug Discovery and Development.
Pinheiro et al. (2023)
2 other articles