Research workbench
Linked amidobenzimidazole sting agonist
Analyse Linked amidobenzimidazole sting agonist in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DXL
- Type
- protein
- Length
- 356 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Stimulator of interferon protein
- UniProt
- A0A2R3XZB7
- Ligands
- HG4, CA
- Pockets
- 4 · best druggability 0.50
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Stimulator of interferon protein | protein | 177 | 52% helix, 20% strand | A0A2R3XZB7 |
| B | Stimulator of interferon protein | protein | 179 | 53% helix, 21% strand | A0A2R3XZB7 |
Ligands and binding sites
- HG4 · 1,1'-(butane-1,4-diyl)bis{2-[(1-ethyl-3-methyl-1H-pyrazole-5-carbonyl)amino]-1H-benzimidazole-5-carboxamide} · ligand · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 262 | 0.50 | 0.74 | 32 | HG4 |
| 2 | 96 | 0.37 | 0.75 | 24 | empty |
| 3 | 83 | 0.30 | 0.73 | 17 | empty |
| 4 | 55 | 0.27 | 0.74 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 909 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6DXL · Linked amidobenzimidazole STING agonist · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A2R3XZB7
- Elsewhere: RCSB PDB 6DXL · PDBe 6DXL · UniProt A0A2R3XZB7
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