MolNFT v1 · #134447 · protein
Human DPP4 in complex with ligand 19A
5T4E · Dipeptidyl peptidase 4: “Human DPP4 in complex with ligand 19A”. X-ray diffraction, 3 ligands (75L, NAG, NA), 15 pockets (best druggability 0.75). MolNFT v1 #134447 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5T4E
- 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
- 75L, NAG, NA
- Pockets
- 15 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 18% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dipeptidyl peptidase 4 (EC 3.4.14.5) | protein | 728 | 18% helix, 37% strand | P27487 |
Ligands and binding sites
- 75L · 2-[(3R)-3-aminopiperidin-1-yl]-3-(but-2-yn-1-yl)-6-[(4-methylquinazolin-2-yl)methyl]-6,7,8,9-tetrahydropyrimido[2,1-b]purin-4(3H)-one · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 19 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
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 73 | 0.75 | 0.98 | 23 | empty |
| 2 | 696 | 0.68 | 0.76 | 79 | 75L |
| 3 | 698 | 0.68 | 0.76 | 83 | 75L |
| 4 | 438 | 0.57 | 0.74 | 60 | empty |
| 5 | 252 | 0.54 | 0.76 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 2314 Ų buried · 44 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 glycan, 10 disulfide (N-glycosylation, 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 5T4E · PDBe 5T4E · UniProt P27487
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.