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Crystal structure of DPP8 in complex with 1G244
Analyse Crystal structure of DPP8 in complex with 1G244 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TRX
- Type
- protein
- Length
- 2,523 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, 9XH, NA, PO4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Dipeptidyl peptidase 8 (EC 3.4.14.5) | protein | 839 | 19% helix, 35% strand | Q6V1X1 |
| A | Dipeptidyl peptidase 8 (EC 3.4.14.5) | protein | 843 | 18% helix, 34% strand | Q6V1X1 |
| C | Dipeptidyl peptidase 8 (EC 3.4.14.5) | protein | 841 | 18% helix, 33% strand | Q6V1X1 |
Ligands and binding sites
- TMO · trimethylamine oxide · ligand · 3 copies · chains B, C, A
- 9XH · (2~{S})-2-azanyl-4-[4-[bis(4-fluorophenyl) methyl]piperazin-1-yl]-1-(1,3-dihydroisoindol-2-yl) butane-1,4-dione · ligand · 3 copies · chains B, A, C
- NA · Sodium ion · metal · 3 copies · chains B, A, C
- PO4 · Phosphate ion · ion · 3 copies · chains B, A, 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 | 1013 | 0.83 | 0.84 | 115 | 9XH, PO4 |
| 2 | 1041 | 0.82 | 0.83 | 115 | 9XH, NA, PO4 |
| 3 | 604 | 0.81 | 0.86 | 53 | empty |
| 4 | 130 | 0.81 | 0.98 | 31 | TMO |
| 5 | 1119 | 0.80 | 0.81 | 93 | empty |
Interfaces
2 interfaces between chains.
- B–C · 2417 Ų buried · 28 hydrogen bonds · protein-protein
- B–A · 492 Ų buried · 7 hydrogen bonds · protein-protein
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 6TRX · PDBe 6TRX · UniProt Q6V1X1
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