MolNFT v1 · #172476 · protein
Crystal structure of DPP8 in complex with a 4-oxo-B-lactam based inhibitor, A241
7A3L · Dipeptidyl peptidase 8: “Crystal structure of DPP8 in complex with a 4-oxo-B-lactam based inhibitor, A241”. X-ray diffraction, 3 ligands (TMO, QXN, CL), 20 pockets (best druggability 0.83). MolNFT v1 #172476 on GenesisL1: 3D…
- PDB
- 7A3L
- Type
- protein
- Length
- 2,526 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, QXN, CL
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 17% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Dipeptidyl peptidase 8 (EC 3.4.14.5) | protein | 850 | 17% helix, 33% strand | Q6V1X1 |
| B | Dipeptidyl peptidase 8 (EC 3.4.14.5) | protein | 826 | 17% helix, 36% strand | Q6V1X1 |
Ligands and binding sites
- TMO · trimethylamine oxide · ligand · 4 copies · chains A, B, C
- QXN · 2-ethyl-2-methanoyl-~{N}-[3-[(4-methylpiperazin-1-yl) methyl]phenyl]butanamide · ligand · 3 copies · chains A, B, C
- CL · Chloride ion · ion · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 181 | 0.83 | 0.98 | 30 | empty |
| 2 | 997 | 0.78 | 0.80 | 122 | QXN, GOL, TMO |
| 3 | 121 | 0.77 | 0.96 | 33 | empty |
| 4 | 1160 | 0.76 | 0.78 | 142 | QXN, GOL, TMO |
| 5 | 1099 | 0.76 | 0.78 | 96 | QXN, GOL, TMO |
Interfaces
3 interfaces between chains.
- B–C · 2403 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 914 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 693 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 7A3L · Crystal structure of DPP8 in complex with a 4-oxo-b-lactam based inhibitor, A241 · 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 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 7A3L · PDBe 7A3L · UniProt Q6V1X1
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