MolNFT v1 · #121860 · protein
Human DPP4 in complex with a novel tricyclic hetero-cycle inhibitor
5I7U · Dipeptidyl peptidase 4: “Human DPP4 in complex with a novel tricyclic hetero-cycle inhibitor”. X-ray diffraction, 3 ligands (6AJ, NAG, NA), 15 pockets (best druggability 0.75). MolNFT v1 #121860 on GenesisL1: 3D structure, binding…
- PDB
- 5I7U
- 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
- 6AJ, NAG, NA
- Pockets
- 15 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 18% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dipeptidyl peptidase 4 (EC 3.4.14.5) | protein | 728 | 18% helix, 38% strand | P27487 |
Ligands and binding sites
- 6AJ · 2-({2-[(3R)-3-aminopiperidin-1-yl]-5-methyl-6,9-dioxo-5,6,7,9-tetrahydro-1H-imidazo[1,2-a]purin-1-yl}methyl)-4-fluorobenzonitrile · 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
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 | 71 | 0.75 | 0.98 | 23 | empty |
| 2 | 973 | 0.71 | 0.75 | 97 | 6AJ |
| 3 | 704 | 0.69 | 0.77 | 86 | 6AJ |
| 4 | 254 | 0.54 | 0.77 | 33 | empty |
| 5 | 224 | 0.52 | 0.77 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 2319 Ų buried · 42 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 glycan, 10 disulfide (N-glycosylation, disulfide).
Compared structures
- 5I7U · Human DPP4 in complex with a novel tricyclic hetero-cycle inhibitor · 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 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 5I7U · PDBe 5I7U · UniProt P27487
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