Research workbench
Crystal structure of DPP8 in complex with a 4-oxo-B-lactam based inhibitor, B115
Analyse Crystal structure of DPP8 in complex with a 4-oxo-B-lactam based inhibitor, B115 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7AYR
- Type
- protein
- Length
- 1,606 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptidyl peptidase 8
- EC
- 3.4.14.5
- UniProt
- Q6V1X1
- Ligands
- TMO, S9W, PO4
- Pockets
- 19 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 18% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dipeptidyl peptidase 8 (EC 3.4.14.5) | protein | 802 | 18% helix, 35% strand | Q6V1X1 |
| B | Dipeptidyl peptidase 8 (EC 3.4.14.5) | protein | 804 | 18% helix, 36% strand | Q6V1X1 |
Ligands and binding sites
- TMO · trimethylamine oxide · ligand · 2 copies · chains A, B
- S9W · ~{N}-[3-[[4-[(4-bromophenyl)methyl]piperazin-1-yl]methyl]phenyl]-4-methanoyl-oxane-4-carboxamide · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 129 | 0.79 | 0.97 | 33 | empty |
| 2 | 664 | 0.74 | 0.80 | 88 | TMO |
| 3 | 448 | 0.72 | 0.82 | 55 | S9W |
| 4 | 502 | 0.67 | 0.78 | 39 | empty |
| 5 | 275 | 0.57 | 0.77 | 41 | S9W |
Interfaces
1 interface between chains.
- A–B · 1509 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7AYR · Crystal structure of DPP8 in complex with a 4-oxo-b-lactam based inhibitor, B115 · the same entry in another collection · chain A against A, TM-score 1.00
- Q6V1X1 · AlphaFold monomer V2.0 prediction for dipeptidyl peptidase 8 (Q6V1X1) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q6V1X1
- Elsewhere: RCSB PDB 7AYR · PDBe 7AYR · UniProt Q6V1X1
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