› 5seq

X-ray diffraction
2.18Å resolution

CRYSTAL STRUCTURE OF HUMAN PHOSPHODIESTERASE 10 IN COMPLEX WITH c1(nn(c(n1)CCc2nn3c(n2)c(nc(c3C)C)C)C)N4CCCC4, micromolar IC50=0.037262

Released:
DOI: 10.2210/pdb5seq/pdb
PDB entry 5seq coloured by chain, front view.
PDB entry 5seq coloured by chain, side view.
PDB entry 5seq coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
A high quality, industrial data set for binding affinity prediction: performance comparison in different early drug discovery scenarios.
Tosstorff A, Rudolph MG, Cole JC, Reutlinger M, Kramer C, Schaffhauser H, Nilly A, Flohr A, Kuhn B
J Comput Aided Mol Des (2022)
PMID: 36153472

Function and Biology Details

Reaction catalysed: 
Nucleoside 3',5'-cyclic phosphate + H(2)O = nucleoside 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-195088 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 343 amino acids
Theoretical weight: 39.41 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9Y233 (Residues: 715-1055; Coverage: 32%)
Gene name: PDE10A

Ligands and Environments

3 bound ligands:
Ligand ZN 4 x ZN
Ligand MG 4 x MG
Ligand IGO 4 x IGO
1 modified residue:
Ligand CME 4 x CME

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X10SA
Spacegroup: R3
Unit cell:
a: 135.275Å b: 135.275Å c: 235.377Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.175 0.172 0.229
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

8 citation in other articles

Combining IC50 or Ki Values from Different Sources Is a Source of Significant Noise.
Landrum et al. (2024)
7 more

1 mention without citation

Identifying virulence determinants of multidrug-resistant Klebsiella pneumoniae in Galleria mellonella.
Bruchmann et al. (2021)