› 6nji

X-ray diffraction
2.45Å resolution

Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with T-49

Released:
DOI: 10.2210/pdb6nji/pdb
PDB entry 6nji coloured by chain, front view.
PDB entry 6nji coloured by chain, side view.
PDB entry 6nji coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Design and Synthesis of Selective Phosphodiesterase 4D (PDE4D) Allosteric Inhibitors for the Treatment of Fragile X Syndrome and Other Brain Disorders.
Gurney ME, Nugent RA, Mo X, Sindac JA, Hagen TJ, Fox D, O'Donnell JM, Zhang C, Xu Y, Zhang HT, Groppi VE, Bailie M, White RE, Romero DL, Vellekoop AS, Walker JR, Surman MD, Zhu L, Campbell RF
J Med Chem 62 4884-4901 (2019)
PMID: 31013090

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
Molecule details ›
Chains: A, B
Length: 370 amino acids
Theoretical weight: 42.59 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q08499 (Residues: 380-718, 326-339; Coverage: 44%)
Gene names: DPDE3, PDE4D
Sequence domains: 3'5'-cyclic nucleotide phosphodiesterase
Structure domains: 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain

Ligands and Environments

3 bound ligands:
Ligand ZN 2 x ZN
Ligand MG 2 x MG
Ligand KR4 2 x KR4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-F
Spacegroup: C2
Unit cell:
a: 124.04Å b: 85.66Å c: 83.45Å
α: 90° β: 110.41° γ: 90°
R-values:
R R work R free
0.187 0.184 0.23
Expression system: Trichoplusia ni

Quick links

Citations

6 review citations

PDE4 subtypes in cancer.
Hsien Lai et al. (2020)
5 more

1 mention without citation

Design and Synthesis of Selective Phosphodiesterase 4D (PDE4D) Allosteric Inhibitors for the Treatment of Fragile X Syndrome and Other Brain Disorders.
Gurney et al. (2019)