MolNFT v1 · #172474 · protein
Crystal structure of DPP8 in complex with a 4-oxo-B-lactam based inhibitor, A272
7A3J · Dipeptidyl peptidase 8: “Crystal structure of DPP8 in complex with a 4-oxo-B-lactam based inhibitor, A272”. X-ray diffraction, 3 ligands (QXK, TMO, CL), 20 pockets (best druggability 0.83). MolNFT v1 #172474 on GenesisL1: 3D…
- PDB
- 7A3J
- Type
- protein
- Length
- 2,459 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
- QXK, TMO, CL
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Dipeptidyl peptidase 8 (EC 3.4.14.5) | protein | 820 | 17% helix, 35% strand | Q6V1X1 |
| A | Dipeptidyl peptidase 8 (EC 3.4.14.5) | protein | 827 | 18% helix, 35% strand | Q6V1X1 |
| B | Dipeptidyl peptidase 8 (EC 3.4.14.5) | protein | 812 | 17% helix, 36% strand | Q6V1X1 |
Ligands and binding sites
- QXK · 2-ethyl-2-methanoyl-~{N}-[3-[[4-(naphthalen-1-ylmethyl)piperazin-1-yl]methyl]phenyl]butanamide · ligand · 3 copies · chains C, A, B
- TMO · trimethylamine oxide · ligand · 3 copies · chains C, A, B
- CL · Chloride ion · ion · 3 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 195 | 0.83 | 0.97 | 32 | empty |
| 2 | 125 | 0.77 | 0.96 | 29 | empty |
| 3 | 668 | 0.75 | 0.81 | 61 | QXK, TMO |
| 4 | 458 | 0.69 | 0.80 | 49 | QXK, TMO |
| 5 | 457 | 0.69 | 0.80 | 54 | empty |
Interfaces
2 interfaces between chains.
- C–B · 2231 Ų buried · 23 hydrogen bonds · protein-protein
- C–A · 496 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 7A3J · Crystal structure of DPP8 in complex with a 4-oxo-b-lactam based inhibitor, A272 · 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 7A3J · PDBe 7A3J · UniProt Q6V1X1
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