Research workbench
Crystal structure of DPP8 in complex with a 4-oxo-B-lactam based inhibitor, LMC375
Analyse Crystal structure of DPP8 in complex with a 4-oxo-B-lactam based inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7A3I
- Type
- protein
- Length
- 2,423 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, QXH, NA, CL
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dipeptidyl peptidase 8 (EC 3.4.14.5) | protein | 807 | 18% helix, 34% strand | Q6V1X1 |
| B | Dipeptidyl peptidase 8 (EC 3.4.14.5) | protein | 808 | 17% helix, 35% strand | Q6V1X1 |
| C | Dipeptidyl peptidase 8 (EC 3.4.14.5) | protein | 808 | 17% helix, 34% strand | Q6V1X1 |
Ligands and binding sites
- TMO · trimethylamine oxide · ligand · 3 copies · chains A, B, C
- QXH · ~{N}-[3,5-bis[[4-[(4-bromophenyl)methyl]piperazin-1-yl]methyl]phenyl]-2-ethyl-2-methanoyl-butanamide · ligand · 3 copies · chains A, B, C
- NA · Sodium ion · metal · 3 copies · chains A, B, C
- CL · Chloride ion · ion · 3 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 133 | 0.79 | 0.97 | 35 | empty |
| 2 | 989 | 0.76 | 0.79 | 106 | TMO |
| 3 | 610 | 0.74 | 0.81 | 73 | TMO |
| 4 | 429 | 0.69 | 0.81 | 48 | empty |
| 5 | 260 | 0.69 | 0.84 | 42 | QXH |
Interfaces
2 interfaces between chains.
- B–C · 1544 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 510 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 7A3I · Crystal structure of DPP8 in complex with a 4-oxo-b-lactam based inhibitor, LMC375 · 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 7A3I · PDBe 7A3I · UniProt Q6V1X1
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