Complex 8oly
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 | 3.11 |
| System mass | 131.57 kDa |
| Deposition year | 2023 |
| Molecule type | RNA |
| # RNA entities | 1 |
| Organism | Oceanobacillus |
| RCSB PDB Entry | 8oly |
| 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 | . / 447 |
| Chain | WA / 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 | 105.30 Å3 |
| Hydrophobicity | 0.013 |
| Hydrophilicity | 1.172 |
| Buriedness | 0.667 |
| Don/acc character | 2.123 |
| SiteScore | 0.740 |
| D Score | 0.459 |
| Kd | — |
| Compound | EPE |
| Residue | . / 449 |
| Chain | YA / 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 | 102.56 Å3 |
| Hydrophobicity | 0.006 |
| Hydrophilicity | 0.819 |
| Buriedness | 0.500 |
| Don/acc character | 3.110 |
| SiteScore | 0.983 |
| D Score | 0.874 |
| Kd | — |
| Compound | EPE |
| Residue | . / 454 |
| Chain | DB / 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 | - |
| Hydrophobicity | - |
| Hydrophilicity | - |
| Buriedness | - |
| Don/acc character | - |
| SiteScore | - |
| D Score | - |
| Kd | — |
| Compound | SPM |
| Residue | . / 452 |
| Chain | BB / 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 | 244.22 Å3 |
| Hydrophobicity | 0.046 |
| Hydrophilicity | 1.099 |
| Buriedness | 0.666 |
| Don/acc character | 0.989 |
| SiteScore | 0.829 |
| D Score | 0.598 |
| Kd | — |
| Compound | SPM |
| Residue | . / 453 |
| Chain | CB / 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 | 236.67 Å3 |
| Hydrophobicity | 0.137 |
| Hydrophilicity | 1.083 |
| Buriedness | 0.670 |
| Don/acc character | 1.872 |
| SiteScore | 0.819 |
| D Score | 0.589 |
| Kd | — |