MolNFT v1 · #184690 · protein
Crystal structure of DPP8 in complex with a 4-oxo-B-lactam based inhibitor, L84
7OZ7 · Dipeptidyl peptidase 8: “Crystal structure of DPP8 in complex with a 4-oxo-B-lactam based inhibitor, L84”. X-ray diffraction, 2 ligands (MQ2, TMO), 17 pockets (best druggability 0.78). MolNFT v1 #184690 on GenesisL1: 3D structure…
- PDB
- 7OZ7
- Type
- protein
- Length
- 1,608 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
- MQ2, TMO
- Pockets
- 17 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 18% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dipeptidyl peptidase 8 (EC 3.4.14.5) | protein | 804 | 18% helix, 36% strand | Q6V1X1 |
| B | Dipeptidyl peptidase 8 (EC 3.4.14.5) | protein | 804 | 19% helix, 35% strand | Q6V1X1 |
Ligands and binding sites
- MQ2 · ~{N}-[3-[[4-[(4-bromophenyl)methyl]piperazin-1-yl]methyl]phenyl]-2-ethyl-2-methanoyl-butanamide · ligand · 2 copies · chains A, B
- TMO · trimethylamine oxide · ligand · 2 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 130 | 0.78 | 0.96 | 33 | empty |
| 2 | 362 | 0.69 | 0.82 | 52 | empty |
| 3 | 900 | 0.67 | 0.73 | 64 | empty |
| 4 | 434 | 0.66 | 0.79 | 44 | empty |
| 5 | 436 | 0.65 | 0.78 | 64 | MQ2, TMO |
Interfaces
1 interface between chains.
- A–B · 1531 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7OZ7 · Crystal structure of DPP8 in complex with a 4-oxo-b-lactam based inhibitor, L84 · 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 7OZ7 · PDBe 7OZ7 · UniProt Q6V1X1
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