Complex 9pii
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 | 2.40 |
| System mass | 2183.65 kDa |
| Deposition year | 2025 |
| Molecule type | RNA/Protein |
| # RNA entities | 1 |
| Organism | Escherichia |
| RCSB PDB Entry | 9pii |
| Reference | Devarkar Swapnil C., Lomakin Ivan B., Wang Jimin, Grada Ayman, Bunick Christopher G.. 2026. Dual site targeting of the bacterial 70S ribosome by tetracyclines Nature Communications |
| Equivalence Class |
NR_all_83717.187,
NR_all_56726.172
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 | V7A |
| Residue | . / 1674 |
| Chain | YD / A |
| Non-redundant | True |
| Interacting RNA chains | AA/X, F/A |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | F/A: rRNA, AA/X: mRNA |
| RNA family global | multiple |
| Volume | 210.60 Å3 |
| Hydrophobicity | 0.479 |
| Hydrophilicity | 0.907 |
| Buriedness | 0.739 |
| Don/acc character | 2.096 |
| SiteScore | 1.057 |
| D Score | 0.900 |
| Kd | — |
| Compound | V7A |
| Residue | . / 3008 |
| Chain | TE / a |
| Non-redundant | True |
| Interacting RNA chains | CA/a |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | CA/a: rRNA |
| RNA family global | rRNA |
| Volume | 252.79 Å3 |
| Hydrophobicity | 0.297 |
| Hydrophilicity | 0.957 |
| Buriedness | 0.667 |
| Don/acc character | 3.283 |
| SiteScore | 1.047 |
| D Score | 0.902 |
| Kd | — |