Crystal structure of human PDE4B with 5-[3-[(1S,2S,4R)- BICYCLO[2.2.1]HEPT-2-yloxy]-4-methoxyp HENYL]TETRAHYDRO-2(1H)- pyrimidinone reveals ordering of the C-terminal helix residues 502- 509.

Structure

x-ray diffraction · 2 distinct chains · 66% helix, 1% strand (DSSP).

Ligands and binding sites

• 0CP · 5-{3-[(1S,2S,4R)-bicyclo[2.2.1]hept-2-yloxy]-4-methoxyphenyl}tetrahydropyrimidin-2(1H)-one · ligand · 2 copies · chains A, B
• ZN · Zinc ion · metal · 2 copies · chains A, B
• MG · Magnesium ion · metal · 2 copies · chains A, B
• B3P · 2-[3-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-propylamino]-2-hydroxymethyl-propane-1,3-diol · additive · chains B

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

Pockets

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 873 Ų buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

• 3KKT · Crystal structure of human PDE4b with 5-[3-[(1S,2S,4R)-Bicyclo[2.2.1]hept-2-yloxy]-4-metho… · the same entry in another collection · chain A against A, TM-score 1.00
• Q07343 · AlphaFold monomer V2.0 prediction for camp-specific 3',5'-cyclic phosphodiesterase 4B… · a predicted model of the same protein · chain B against A, TM-score 0.94

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 Q07343
• Elsewhere: RCSB PDB 3KKT · PDBe 3KKT · UniProt Q07343