MolNFT v1 · #172475 · protein
Crystal structure of DPP8 in complex with a B-lactam based inhibitor, A296.1
7A3K · Dipeptidyl peptidase 8: “Crystal structure of DPP8 in complex with a B-lactam based inhibitor, A296.1”. X-ray diffraction, 4 ligands (TMO, QX8, NA), 20 pockets (best druggability 0.83). MolNFT v1 #172475 on GenesisL1: 3D structure…
- PDB
- 7A3K
- Type
- protein
- Length
- 2,462 residues
- Chains
- 3
- 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, QX8, NA, CL
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 18% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, A | Dipeptidyl peptidase 8 (EC 3.4.14.5) | protein | 821 | 18% helix, 35% strand | Q6V1X1 |
| B | Dipeptidyl peptidase 8 (EC 3.4.14.5) | protein | 820 | 18% helix, 35% strand | Q6V1X1 |
Ligands and binding sites
- TMO · trimethylamine oxide · ligand · 3 copies · chains C, A, B
- QX8 · 1-[3-[[4-[(4-bromophenyl)methyl]piperazin-1-yl]methyl]phenyl]azetidin-2-one · ligand · 3 copies · chains C, A, B
- NA · Sodium ion · metal · 3 copies · chains C, A, B
- CL · Chloride ion · ion · 8 copies · chains C, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 188 | 0.83 | 0.97 | 33 | empty |
| 2 | 141 | 0.79 | 0.97 | 33 | empty |
| 3 | 865 | 0.79 | 0.82 | 103 | TMO, QX8 |
| 4 | 876 | 0.78 | 0.81 | 94 | TMO, QX8 |
| 5 | 1042 | 0.76 | 0.79 | 117 | TMO |
Interfaces
2 interfaces between chains.
- C–B · 2396 Ų buried · 26 hydrogen bonds · protein-protein
- C–A · 500 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 7A3K · Crystal structure of DPP8 in complex with a b-lactam based inhibitor, A296.1 · the same entry in another collection · chain C against C, TM-score 1.00
- Q6V1X1 · AlphaFold monomer V2.0 prediction for dipeptidyl peptidase 8 (Q6V1X1) · a predicted model of the same protein · chain B 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 7A3K · PDBe 7A3K · UniProt Q6V1X1
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