› 6rcw

X-ray diffraction
2.08Å resolution

Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-053

Released:
DOI: 10.2210/pdb6rcw/pdb
PDB entry 6rcw coloured by chain, front view.
PDB entry 6rcw coloured by chain, side view.
PDB entry 6rcw coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Alkynamide phthalazinones as a new class of TbrPDEB1 inhibitors (Part 2).
de Heuvel E, Singh AK, Boronat P, Kooistra AJ, van der Meer T, Sadek P, Blaazer AR, Shaner NC, Bindels DS, Caljon G, Maes L, Sterk GJ, Siderius M, Oberholzer M, de Esch IJP, Brown DG, Leurs R
Bioorg Med Chem 27 4013-4029 (2019)
PMID: 31378593

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: 364 amino acids
Theoretical weight: 41.81 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q08499 (Residues: 381-740; Coverage: 45%)
Gene names: DPDE3, PDE4D
Sequence domains: 3'5'-cyclic nucleotide phosphodiesterase

Ligands and Environments

7 bound ligands:
Ligand ZN 4 x ZN
Ligand MG 4 x MG
Ligand EDO 38 x EDO
Ligand PEG 3 x PEG
Ligand DTT 2 x DTT
Ligand EPE 2 x EPE
Ligand JX2 3 x JX2
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: P212121
Unit cell:
a: 99.894Å b: 110.505Å c: 160.694Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.175 0.172 0.221
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

Tackling Sleeping Sickness: Current and Promising Therapeutics and Treatment Strategies.
Jamabo et al. (2023)
5 other articles