Complex 8olz
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 | 3.31 |
| System mass | 131.55 kDa |
| Deposition year | 2023 |
| Molecule type | RNA |
| # RNA entities | 1 |
| Organism | Oceanobacillus |
| RCSB PDB Entry | 8olz |
| 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 | . / 450 |
| Chain | ZA / 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 | 46.31 Å3 |
| Hydrophobicity | 0.018 |
| Hydrophilicity | 1.112 |
| Buriedness | 0.564 |
| Don/acc character | 3.876 |
| SiteScore | 0.591 |
| D Score | 0.315 |
| Kd | — |
| Compound | SPM |
| 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 | 372.16 Å3 |
| Hydrophobicity | 0.095 |
| Hydrophilicity | 1.139 |
| Buriedness | 0.697 |
| Don/acc character | 1.506 |
| SiteScore | 1.025 |
| D Score | 0.828 |
| Kd | — |
| Compound | VTE |
| Residue | . / 453 |
| Chain | CB / A |
| Non-redundant | False |
| Interacting RNA chains | B/B, A/A |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | A/A: ribozyme, B/B: ribozyme |
| RNA family global | ribozyme |
| Volume | 239.07 Å3 |
| Hydrophobicity | 0.051 |
| Hydrophilicity | 1.412 |
| Buriedness | 0.665 |
| Don/acc character | 4.356 |
| SiteScore | 1.055 |
| D Score | 0.785 |
| Kd | — |