Complex 8run
Legend
Pocket colors by molecule type
RNA
Protein
DNA
These colors appear when a pocket is selected (the structure fades to show the pocket surface). Colors from the molecule-type palette (RNA / protein / DNA).
System information
| Experimental technique | X-ray |
| Experimental resolution | 3.73 |
| System mass | 129.72 kDa |
| Deposition year | 2024 |
| Molecule type | RNA |
| # RNA entities | 1 |
| Organism | Oceanobacillus |
| RCSB PDB Entry | 8run |
| Reference | Silvestri Ilaria, Manigrasso Jacopo, Andreani Alessandro, Brindani Nicoletta, Mas Caroline, Reiser Jean-Baptiste, Vidossich Pietro, Martino Gianfranco, McCarthy Andrew A., De Vivo Marco, Marcia Marco. 2024. Targeting the conserved active site of splicing machines with specific and selective small molecule modulators Nature Communications |
| Equivalence Class |
NR_all_35054.12
BGSU version: 4.52 |
Pockets List
Legend
Cell colors for SiteScore and D Score:
Favourable
Intermediate
Unfavourable
Not available
| Score | Threshold | Meaning |
|---|---|---|
| SiteScore | < 0.8 | Non-drug binding site |
| SiteScore | 0.8 – 1.0 | Potential drug binding site |
| SiteScore | > 1.0 | Promising binding site |
| D Score | < 0.83 | Undruggable |
| D Score | 0.83 – 0.98 | Difficult |
| D Score | > 0.98 | Druggable |
Tick a pocket below to highlight it in the 3D structure above.
| Compound | EPE |
| Residue | . / 401 |
| Chain | B / A |
| Non-redundant | False |
| Interacting RNA chains | A/A |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | A/A: ribozyme |
| RNA family global | ribozyme |
| Volume | 30.18 Å3 |
| Hydrophobicity | 0.032 |
| Hydrophilicity | 1.174 |
| Buriedness | 0.601 |
| Don/acc character | 3.053 |
| SiteScore | 0.606 |
| D Score | 0.304 |
| Kd | — |
| Compound | EPE |
| Residue | . / 402 |
| Chain | C / A |
| Non-redundant | False |
| Interacting RNA chains | A/A |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | A/A: ribozyme |
| RNA family global | ribozyme |
| Volume | 391.36 Å3 |
| Hydrophobicity | 0.061 |
| Hydrophilicity | 0.951 |
| Buriedness | 0.684 |
| Don/acc character | 2.844 |
| SiteScore | 1.011 |
| D Score | 0.852 |
| Kd | — |
| Compound | VTR |
| Residue | . / 403 |
| Chain | D / A |
| Non-redundant | False |
| Interacting RNA chains | A/A |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | A/A: ribozyme |
| RNA family global | ribozyme |
| Volume | 289.49 Å3 |
| Hydrophobicity | 0.003 |
| Hydrophilicity | 1.263 |
| Buriedness | 0.648 |
| Don/acc character | 1.275 |
| SiteScore | 1.014 |
| D Score | 0.786 |
| Kd | — |