MolNFT v1 · #151485 · protein
Crystal structure of DPP8 in complex with val-boropro
6HP8 · Dipeptidyl peptidase 8: “Crystal structure of DPP8 in complex with val-boropro”. X-ray diffraction, 2 ligands (GK2, NA), 20 pockets (best druggability 0.82). MolNFT v1 #151485 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6HP8
- Type
- protein
- Length
- 2,508 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
- GK2, NA
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dipeptidyl peptidase 8 (EC 3.4.14.5) | protein | 836 | 19% helix, 35% strand | Q6V1X1 |
| B | Dipeptidyl peptidase 8 (EC 3.4.14.5) | protein | 835 | 19% helix, 35% strand | Q6V1X1 |
| C | Dipeptidyl peptidase 8 (EC 3.4.14.5) | protein | 837 | 19% helix, 36% strand | Q6V1X1 |
Ligands and binding sites
- GK2 · [(2~{R})-1-[(2~{R})-2-azanyl-3-methyl-butanoyl]pyrrolidin-2-yl]boronic acid · ligand · 3 copies · chains A, B, C
- NA · Sodium ion · metal · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 15 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 | 987 | 0.82 | 0.84 | 96 | GK2, NA, GOL |
| 2 | 836 | 0.81 | 0.84 | 86 | GK2, GOL |
| 3 | 896 | 0.81 | 0.83 | 91 | GK2, GOL |
| 4 | 813 | 0.81 | 0.84 | 84 | GOL |
| 5 | 599 | 0.81 | 0.86 | 57 | empty |
Interfaces
2 interfaces between chains.
- B–C · 2560 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 435 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
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 6HP8 · PDBe 6HP8 · UniProt Q6V1X1
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