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X-ray diffraction
2.29Å resolution

CRYSTAL STRUCTURE OF HUMAN PHOSPHODIESTERASE 10 IN COMPLEX WITH c2(c(C(=O)NC1COC1)cc3c(c2)nc([nH]3)c4ccccc4)NC(C5=CC(=CN(C5=O)C)Br)=O, micromolar IC50=0.006706

Released:
DOI: 10.2210/pdb5seg/pdb
Model geometry
Fit model/data
PDB entry 5seg coloured by chain, front view.
PDB entry 5seg coloured by chain, side view.
PDB entry 5seg 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: 
[a nucleoside 3',5'-cyclic phosphate + H2O = a nucleoside 5'-phosphate +H(+)., a nucleoside 3',5'-cyclic phosphate + H2O = a nucleoside 5'-phosphate +H(+)., a nucleoside 3',5'-cyclic phosphate + H2O = a nucleoside 5'-phosphate +H(+)., a nucleoside 3',5'-cyclic phosphate + H2O = a nucleoside 5'-phosphate +H(+).]
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 IFN 4 x IFN
1 modified residue:
Ligand CME 4 x CME

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SLS BEAMLINE X10SA
Spacegroup: R3
Unit cell:
a: 135.29Å b: 135.29Å c: 235.561Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.177 0.174 0.231
Expression system: Escherichia coli BL21(DE3)

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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