Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor npd-007

Structure

x-ray diffraction · 4 distinct chains.

Ligands and binding sites

• E8H · 1-(2-{4-[(4as,8ar)-4-(3,4-dimethoxyphenyl)-1-oxo-1,2, 4A,5,8,8A-hexahydrophthalazin-2-yl]piperidin-1-yl}-2-oxoethyl)pyrrolidine-2,5-dione · ligand · 4 copies · chains A, B, C, D
• ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
• MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
• EDO · 1,2-ethanediol · additive · 59 copies · chains A, C, D, B
• EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 5 copies · chains A, B, C, D
• PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, C, B, D
• PG4 · Tetraethylene glycol · additive · chains C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Compared structures

• 6FW3 · Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-007 · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt Q08499
• Elsewhere: RCSB PDB 6FW3 · PDBe 6FW3 · UniProt Q08499