Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor npd-053

Structure

x-ray diffraction · 3 distinct chains.

Ligands and binding sites

• JX2 · 3-[5-[(4~{a}~{R},8~{a}~{S})-3-cycloheptyl-4-oxidanylidene-4~{a},5,8,8~{a}-tetrahydrophthalazin-1-yl]-2-methoxy-phenyl]-~{N}-(furan-2-ylmethyl)prop-2-ynamide · ligand · 3 copies · chains 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 · 38 copies · chains A, B, C, D
• PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, D
• DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · 2 copies · chains A, C, B, D
• EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains B, C

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

Compared structures

• 6RCW · Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-053 · 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 6RCW · PDBe 6RCW · UniProt Q08499