Crystal structure of DPP8 in complex with a 4-oxo-B-lactam based inhibitor, 91

Structure

x-ray diffraction · 2 distinct chains · 18% helix, 36% strand (DSSP).

Ligands and binding sites

• TMO · trimethylamine oxide · ligand · 4 copies · chains B, A
• QXQ · ~{N}-[3-(7,8-dihydro-5~{H}-[1,3]dioxolo[4,5-g]isoquinolin-6-ylmethyl)phenyl]-2-ethyl-2-methanoyl-butanamide · ligand · 2 copies · chains B, A
• QXT · 1-[3-(7,8-dihydro-5~{H}-[1,3]dioxolo[4,5-g]isoquinolin-6-ylmethyl)phenyl]-3,3-diethyl-azetidine-2,4-dione · ligand · 2 copies · chains B, A
• PO4 · Phosphate ion · ion · 8 copies · chains B, A
• CL · Chloride ion · ion · 2 copies · chains B, A
• GOL · Glycerol · additive · 4 copies · chains B, A

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

Pockets

19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• B–A · 2305 Ų buried · 30 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

• 7A3G · Crystal structure of DPP8 in complex with a 4-oxo-b-lactam based inhibitor, 91 · the same entry in another collection · chain B against B, TM-score 1.00
• Q6V1X1 · AlphaFold monomer V2.0 prediction for dipeptidyl peptidase 8 (Q6V1X1) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q6V1X1
• Elsewhere: RCSB PDB 7A3G · PDBe 7A3G · UniProt Q6V1X1