› 8w4q

X-ray diffraction
1.55Å resolution

Crystal structure of PDE4D complexed with CX-4945

Released:
DOI: 10.2210/pdb8w4q/pdb
PDB entry 8w4q coloured by chain, front view.
PDB entry 8w4q coloured by chain, side view.
PDB entry 8w4q coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Drug repurposing and structure-based discovery of new PDE4 and PDE5 inhibitors.
Liu J, Zhang X, Chen G, Shao Q, Zou Y, Li Z, Su H, Li M, Xu Y
Eur J Med Chem 262 115893 (2023)
PMID: 37918035

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

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: 349 amino acids
Theoretical weight: 40.1 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q08499 (Residues: 388-715; Coverage: 41%)
Gene names: DPDE3, PDE4D
Sequence domains: 3'5'-cyclic nucleotide phosphodiesterase

Ligands and Environments

4 bound ligands:
Ligand MG 2 x MG
Ligand ZN 2 x ZN
Ligand 3NG 2 x 3NG
Ligand EDO 6 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL10U2
Spacegroup: P212121
Unit cell:
a: 57.509Å b: 79.99Å c: 162.723Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.226 0.226 0.24
Expression system: Escherichia coli BL21(DE3)

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