DPP1 in complex with inhibitor

Structure

x-ray diffraction · 3 distinct chains · 17% helix, 34% strand (DSSP).

Ligands and binding sites

• K9W · (2~{S})-~{N}-[(2~{S})-1-azanyl-3-[4-(4-cyanophenyl) phenyl]propan-2-yl]pyrrolidine-2-carboxamide · ligand · chains A, B, C
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, C, B
• CL · Chloride ion · ion · chains B, C
• DMS · Dimethyl sulfoxide · additive · 2 copies · chains A, B, C
• GOL · Glycerol · additive · chains A, 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, 1 with a druggability of 0.5 or more.

Interfaces

3 interfaces between chains.

• B–C · 3029 Ų buried · 55 hydrogen bonds · protein-protein
• A–B · 1007 Ų buried · 17 hydrogen bonds · protein-protein
• A–C · 348 Ų buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide, 3 glycan, 1 covalent (disulfide, N-glycosylation, covalent ligand).

Compared structures

• 6RN7 · DPP1 in complex with inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
• P53634 · AlphaFold monomer V2.0 prediction for dipeptidyl peptidase 1 (P53634) · a predicted model of the same protein · chain B 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 P53634
• Elsewhere: RCSB PDB 6RN7 · PDBe 6RN7 · UniProt P53634