MolNFT v1 · #184468 · protein
Crystal structure of DPP8 in complex with a 4-oxo-B-lactam based inhibitor, B142
7OR4 · Dipeptidyl peptidase 8: “Crystal structure of DPP8 in complex with a 4-oxo-B-lactam based inhibitor, B142”. X-ray diffraction, 2 ligands (TMO, 2YI), 16 pockets (best druggability 0.77). MolNFT v1 #184468 on GenesisL1: 3D structure…
- PDB
- 7OR4
- Type
- protein
- Length
- 1,620 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, 2YI
- Pockets
- 16 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 18% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Dipeptidyl peptidase 8 (EC 3.4.14.5) | protein | 815 | 18% helix, 34% strand | Q6V1X1 |
| A | Dipeptidyl peptidase 8 (EC 3.4.14.5) | protein | 805 | 18% helix, 36% strand | Q6V1X1 |
Ligands and binding sites
- TMO · trimethylamine oxide · ligand · 2 copies · chains B, A
- 2YI · Methyl 3-[4-[(4-bromophenyl)methyl]piperazin-1-yl]carbonyl-5-[(2-ethyl-2-methanoyl-butanoyl) amino]benzoate · ligand · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 115 | 0.77 | 0.96 | 31 | empty |
| 2 | 336 | 0.74 | 0.85 | 43 | 2YI |
| 3 | 388 | 0.72 | 0.84 | 46 | empty |
| 4 | 465 | 0.72 | 0.82 | 55 | empty |
| 5 | 462 | 0.68 | 0.79 | 42 | empty |
Interfaces
1 interface between chains.
- B–A · 1508 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7OR4 · Crystal structure of DPP8 in complex with a 4-oxo-b-lactam based inhibitor, B142 · the same entry in another collection · chain B against B, 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 7OR4 · PDBe 7OR4 · UniProt Q6V1X1
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