› 6imb

X-ray diffraction
1.55Å resolution

Crystal structure of PDE4D complexed with a novel inhibitor

Released:
DOI: 10.2210/pdb6imb/pdb
PDB entry 6imb coloured by chain, front view.
PDB entry 6imb coloured by chain, side view.
PDB entry 6imb coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure-Aided Identification and Optimization of Tetrahydro-isoquinolines as Novel PDE4 Inhibitors Leading to Discovery of an Effective Antipsoriasis Agent.
Zhang X, Dong G, Li H, Chen W, Li J, Feng C, Gu Z, Zhu F, Zhang R, Li M, Tang W, Liu H, Xu Y
J Med Chem 62 5579-5593 (2019)
PMID: 31099559

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: 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 ZN 2 x ZN
Ligand MG 4 x MG
Ligand AH9 2 x AH9
Ligand EDO 15 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL19U1
Spacegroup: P212121
Unit cell:
a: 58.497Å b: 80.432Å c: 163.532Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.201 0.2 0.219
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 review citations

Berberine and its derivatives represent as the promising therapeutic agents for inflammatory disorders.
Lu et al. (2022)
1 more