Complex 9dp7
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 | Electron Microscopy |
| Experimental resolution | 2.38 |
| System mass | 3191.54 kDa |
| Deposition year | 2024 |
| Molecule type | RNA/Protein |
| # RNA entities | 1 |
| Organism | Saccharomyces |
| RCSB PDB Entry | 9dp7 |
| Reference | Zhao Yu, Xu Chong, Chen Xin, Jin Hong, Li Hong. 2025. Structural basis for hygromycin B inhibition of yeast pseudouridine-deficient ribosomes Science Advances |
| Equivalence Class |
NR_all_03510.74,
NR_all_04576.5
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 | HYG |
| Residue | . / 1801 |
| Chain | EC / B5 |
| Non-redundant | True |
| Interacting RNA chains | BC/EC, HA/B5 |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | BC/EC: rRNA, HA/B5: rRNA |
| RNA family global | rRNA |
| Volume | 514.84 Å3 |
| Hydrophobicity | 0.168 |
| Hydrophilicity | 0.944 |
| Buriedness | 0.656 |
| Don/acc character | 2.191 |
| SiteScore | 1.140 |
| D Score | 1.025 |
| Kd | — |