Crystal structure of human depiptidyl peptidase IV (dpp-4) in complex with vildagliptin

Structure

x-ray diffraction · 1 distinct chain · 18% helix, 37% strand (DSSP).

Ligands and binding sites

• LF7 · 2-{[(1r,3s,5R,7S)-3-hydroxytricyclo[3.3.1.1~3,7~]decan-1-yl]amino}-1-{(2S)-2-[(E)-iminomethyl]pyrrolidin-1-yl}ethan-1-o ne · ligand · 2 copies · chains A, B
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 19 copies · chains A, B
• FUL · beta-L-fucopyranose · sugar · 2 copies · chains A, B
• GOL · Glycerol · additive · 2 copies · chains A, B

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 2315 Ų buried · 44 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 13 glycan, 10 disulfide, 2 covalent (N-glycosylation, disulfide, covalent ligand).

Compared structures

• 3W2T · Crystal structure of human depiptidyl peptidase IV (DPP-4) in complex with vildagliptin · the same entry in another collection · chain A against A, TM-score 1.00
• P27487 · AlphaFold monomer V2.0 prediction for dipeptidyl peptidase 4 (P27487) · 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 P27487
• Elsewhere: RCSB PDB 3W2T · PDBe 3W2T · UniProt P27487