› 3g4l

X-ray diffraction
2.5Å resolution

Crystal structure of human phosphodiesterase 4d with roflumilast

Released:
DOI: 10.2210/pdb3g4l/pdb
PDB entry 3g4l coloured by chain, front view.
PDB entry 3g4l coloured by chain, side view.
PDB entry 3g4l coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Design of phosphodiesterase 4D (PDE4D) allosteric modulators for enhancing cognition with improved safety.
Burgin AB, Magnusson OT, Singh J, Witte P, Staker BL, Bjornsson JM, Thorsteinsdottir M, Hrafnsdottir S, Hagen T, Kiselyov AS, Stewart LJ, Gurney ME
Nat Biotechnol 28 63-70 (2010)
PMID: 20037581

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, C, D
Molecule details ›
Chains: A, B, C, D
Length: 381 amino acids
Theoretical weight: 43.79 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q08499 (Residues: 380-753; Coverage: 46%)
Gene names: DPDE3, PDE4D
Sequence domains: 3'5'-cyclic nucleotide phosphodiesterase
Structure domains: 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain

Ligands and Environments

5 bound ligands:
Ligand ZN 4 x ZN
Ligand MG 4 x MG
Ligand SO4 4 x SO4
Ligand ROF 4 x ROF
Ligand EDO 8 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.1
Spacegroup: P212121
Unit cell:
a: 99.665Å b: 111.952Å c: 161.701Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.217 0.214 0.259
Expression system: Spodoptera frugiperda

Quick links

Citations

50 review citations

Cognitive dysfunction in psychiatric disorders: characteristics, causes and the quest for improved therapy.
Millan et al. (2012)
49 more

3 mentions without citation

Pharmacological and molecular dynamics analyses of differences in inhibitor binding to human and nematode PDE4: Implications for management of parasitic nematodes.
Schuster et al. (2019)
2 more