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The structure of DPP4 in complex with piperidine fused benzimidazole 25
Analyse The structure of DPP4 in complex with piperidine fused benzimidazole 25 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HAB
- Type
- protein
- Length
- 1,456 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptidyl peptidase 4 soluble form
- UniProt
- P27487
- Ligands
- 677, NAG, NA
- Pockets
- 16 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 18% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dipeptidyl peptidase 4 soluble form | protein | 728 | 18% helix, 37% strand | P27487 |
Ligands and binding sites
- 677 · (2R,3R)-7-(methylsulfonyl)-3-(2,4,5-trifluorophenyl)-1,2,3,4-tetrahydropyrido[1,2-a]benzimidazol-2-amine · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 22 copies · chains A, B
- NA · Sodium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 58 | 0.73 | 0.98 | 16 | empty |
| 2 | 750 | 0.69 | 0.76 | 91 | 677 |
| 3 | 760 | 0.69 | 0.76 | 87 | 677 |
| 4 | 248 | 0.52 | 0.76 | 35 | empty |
| 5 | 181 | 0.52 | 0.78 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 2306 Ų buried · 47 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 glycan, 10 disulfide (N-glycosylation, disulfide).
Compared structures
- 3HAB · The structure of DPP4 in complex with piperidine fused benzimidazole 25 · the same entry in another collection · chain B against B, TM-score 1.00
- P27487 · AlphaFold monomer V2.0 prediction for dipeptidyl peptidase 4 (P27487) · a predicted model of the same protein · 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 P27487
- Elsewhere: RCSB PDB 3HAB · PDBe 3HAB · UniProt P27487
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