MolNFT v1 · #50389 · protein
Crystal structure of complex of human DPP4 and inhibitor
2RGU · Dipeptidyl peptidase 4: “Crystal structure of complex of human DPP4 and inhibitor”. X-ray diffraction, 2 ligands (356, NAG), 17 pockets (best druggability 0.73). MolNFT v1 #50389 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 2RGU
- Type
- protein
- Length
- 1,456 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptidyl peptidase 4
- EC
- 3.4.14.5
- UniProt
- P27487
- Ligands
- 356, NAG
- Pockets
- 17 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 18% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dipeptidyl peptidase 4 (EC 3.4.14.5) | protein | 728 | 18% helix, 36% strand | P27487 |
Ligands and binding sites
- 356 · 8-[(3R)-3-Aminopiperidin-1-yl]-7-but-2-yn-1-yl-3-methyl-1-[(4-methylquinazolin-2-yl)methyl]-3,7-dihydro-1H-purine-2,6-d ione · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 63 | 0.73 | 0.98 | 22 | empty |
| 2 | 827 | 0.71 | 0.76 | 88 | 356 |
| 3 | 762 | 0.70 | 0.76 | 88 | 356 |
| 4 | 432 | 0.56 | 0.73 | 54 | empty |
| 5 | 247 | 0.53 | 0.76 | 35 | empty |
Interfaces
1 interface between chains.
- A–B · 2343 Ų buried · 40 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
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 2RGU · PDBe 2RGU · UniProt P27487
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.