MolNFT v1 · #122552 · protein
Human DPP4 in complex with a novel 5,5,6-tricyclic pyrrolidine inhibitor
5ISM · Dipeptidyl peptidase 4: “Human DPP4 in complex with a novel 5,5,6-tricyclic pyrrolidine inhibitor”. X-ray diffraction, 3 ligands (6DG, NAG, NA), 17 pockets (best druggability 0.75). MolNFT v1 #122552 on GenesisL1: 3D structure…
- PDB
- 5ISM
- 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
- 6DG, NAG, NA
- Pockets
- 17 · 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
- 6DG · (2R,3S,5R)-2-(2,5-difluorophenyl)-5-(7H-pyrrolo[3',4':3,4]pyrazolo[1,5-a]pyrimidin-8(9H)-yl)oxan-3-amine · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 18 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
17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 76 | 0.75 | 0.97 | 24 | empty |
| 2 | 812 | 0.70 | 0.76 | 97 | 6DG |
| 3 | 691 | 0.69 | 0.77 | 91 | 6DG |
| 4 | 399 | 0.55 | 0.73 | 48 | empty |
| 5 | 259 | 0.54 | 0.76 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 2287 Ų buried · 41 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 glycan, 10 disulfide (N-glycosylation, disulfide).
Compared structures
- 5ISM · Human DPP4 in complex with a novel 5,5,6-tricyclic pyrrolidine 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 5ISM · PDBe 5ISM · UniProt P27487
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.