› 6gxq

X-ray diffraction
1.96Å resolution

Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-1335

Released:
DOI: 10.2210/pdb6gxq/pdb
PDB entry 6gxq coloured by chain, front view.
PDB entry 6gxq coloured by chain, side view.
PDB entry 6gxq coloured by chain, top view.
Source organism: Trypanosoma brucei
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

Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-570647 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Phosphodiesterase Chains: A, B
Molecule details ›
Chains: A, B
Length: 360 amino acids
Theoretical weight: 40.62 KDa
Source organism: Trypanosoma brucei
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8WQX9 (Residues: 565-918; Coverage: 38%)
Gene name: PDEB1
Sequence domains: 3'5'-cyclic nucleotide phosphodiesterase

Ligands and Environments

5 bound ligands:
Ligand MG 2 x MG
Ligand ZN 2 x ZN
Ligand GAI 5 x GAI
Ligand FFZ 1 x FFZ
Ligand GOL 3 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04-1
Spacegroup: C2
Unit cell:
a: 114.876Å b: 114.424Å c: 68.232Å
α: 90° β: 108.36° γ: 90°
R-values:
R R work R free
0.202 0.2 0.244
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)
4 other articles

1 mention without citation

Exploring the Activity Profile of TbrPDEB1 and hPDE4 Inhibitors Using Free Energy Perturbation.
Zara et al. (2022)