› 6kk0

X-ray diffraction
2.2Å resolution

Crystal structure of PDE4D catalytic domain complexed with compound 4e

Released:
DOI: 10.2210/pdb6kk0/pdb
PDB entry 6kk0 coloured by chain, front view.
PDB entry 6kk0 coloured by chain, side view.
PDB entry 6kk0 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Discovery and Optimization of α-Mangostin Derivatives as Novel PDE4 Inhibitors for the Treatment of Vascular Dementia.
Liang J, Huang YY, Zhou Q, Gao Y, Li Z, Wu D, Yu S, Guo L, Chen Z, Huang L, Liang SH, He X, Wu R, Luo HB
J Med Chem 63 3370-3380 (2020)
PMID: 32115956

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:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-170654 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
3',5'-cyclic-AMP phosphodiesterase 4D Chains: A, B
Molecule details ›
Chains: A, B
Length: 326 amino acids
Theoretical weight: 37.58 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q08499 (Residues: 388-713; Coverage: 40%)
Gene names: DPDE3, PDE4D
Sequence domains: 3'5'-cyclic nucleotide phosphodiesterase

Ligands and Environments

3 bound ligands:
Ligand M36 2 x M36
Ligand ZN 2 x ZN
Ligand MG 2 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: OXFORD DIFFRACTION NOVA
Spacegroup: P212121
Unit cell:
a: 60.365Å b: 77.984Å c: 163.344Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.2 0.198 0.247
Expression system: Escherichia coli BL21

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Citations

1 review citation

Phosphodiesterase-4 Inhibition in Parkinson's Disease: Molecular Insights and Therapeutic Potential.
Roy et al. (2023)
4 other articles