› 5e80

X-ray diffraction
2.6Å resolution

The crystal structure of PDEd in complex with inhibitor-2a

Released:
DOI: 10.2210/pdb5e80/pdb
PDB entry 5e80 coloured by chain, front view.
PDB entry 5e80 coloured by chain, side view.
PDB entry 5e80 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Identification of pyrazolopyridazinones as PDEδ inhibitors.
Papke B, Murarka S, Vogel HA, Martín-Gago P, Kovacevic M, Truxius DC, Fansa EK, Ismail S, Zimmermann G, Heinelt K, Schultz-Fademrecht C, Al Saabi A, Baumann M, Nussbaumer P, Wittinghofer A, Waldmann H, Bastiaens PI
OpenAccess logo Nat Commun 7 11360 (2016)
PMID: 27094677

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-129171 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta Chains: A, B
Molecule details ›
Chains: A, B
Length: 149 amino acids
Theoretical weight: 17.25 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O43924 (Residues: 2-150; Coverage: 99%)
Gene names: PDE6D, PDED
Sequence domains: GMP-PDE, delta subunit
Structure domains: GMP phosphodiesterase, delta subunit

Ligands and Environments

1 bound ligand:
Ligand 5KP 2 x 5KP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X10SA
Spacegroup: P1
Unit cell:
a: 31.76Å b: 40.9Å c: 68.8Å
α: 97.7° β: 102.38° γ: 89.31°
R-values:
R R work R free
0.188 0.185 0.247
Expression system: Escherichia coli

Quick links

Citations

39 review citations

RAS Proteins and Their Regulators in Human Disease.
Simanshu et al. (2017)
38 more

2 mentions without citation

Identification of pyrazolopyridazinones as PDEδ inhibitors.
Papke et al. (2016)
1 more