› 5wh5

X-ray diffraction
1.8Å resolution

Crystal structure of the PDE4D2 catalytic domain in complex with inhibitor (R)-Zl-n-91

Released:
DOI: 10.2210/pdb5wh5/pdb
PDB entry 5wh5 coloured by chain, front view.
PDB entry 5wh5 coloured by chain, side view.
PDB entry 5wh5 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Identification of a PDE4-Specific Pocket for the Design of Selective Inhibitors.
Feng X, Wang H, Ye M, Xu XT, Xu Y, Yang W, Zhang HT, Song G, Ke H
Biochemistry 57 4518-4525 (2018)
PMID: 29975048

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: 327 amino acids
Theoretical weight: 37.71 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q08499 (Residues: 388-714; Coverage: 40%)
Gene names: DPDE3, PDE4D
Sequence domains: 3'5'-cyclic nucleotide phosphodiesterase
Structure domains: 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain

Ligands and Environments

3 bound ligands:
Ligand R91 2 x R91
Ligand ZN 2 x ZN
Ligand MG 3 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: P212121
Unit cell:
a: 59.467Å b: 79.883Å c: 163.444Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.194 0.193 0.214
Expression system: Escherichia coli BL21

Quick links

Citations

1 review citation

The Complexity and Multiplicity of the Specific cAMP Phosphodiesterase Family: PDE4, Open New Adapted Therapeutic Approaches.
Lugnier C. (2022)
4 other articles

2 mentions without citation

In Silico, Ex Vivo and In Vivo Studies of Roflumilast as a Potential Antidiarrheal and Antispasmodic agent: Inhibition of the PDE-4 Enzyme and Voltage-gated Ca++ ion Channels.
Rehman et al. (2020)
1 more