Complex 8vty
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 | 2.60 |
| System mass | 4427.77 kDa |
| Deposition year | 2024 |
| Molecule type | RNA/Protein |
| # RNA entities | 1 |
| Organism | Thermus |
| RCSB PDB Entry | 8vty |
| Reference | Aleksandrova Elena V., Ma Cong-Xuan, Klepacki Dorota, Alizadeh Faezeh, Vázquez-Laslop Nora, Liang Jian-Hua, Polikanov Yury S., Mankin Alexander S.. 2024. Macrolones target bacterial ribosomes and DNA gyrase and can evade resistance mechanisms Nature Chemical Biology |
| Equivalence Class |
NR_all_97519.80,
NR_all_42622.80
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 | ARG |
| Residue | . / 230 |
| Chain | XSA / 1B |
| Non-redundant | True |
| Interacting RNA chains | B/1B |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | B/1B: rRNA |
| RNA family global | rRNA |
| Volume | 121.08 Å3 |
| Hydrophobicity | 0.017 |
| Hydrophilicity | 2.150 |
| Buriedness | 0.615 |
| Don/acc character | 1.100 |
| SiteScore | 0.890 |
| D Score | 0.346 |
| Kd | — |
| Compound | ARG |
| Residue | . / 320 |
| Chain | SUA / 1F |
| Non-redundant | True |
| Interacting RNA chains | A/1A |
| RNA environment detailled | protein, ion |
| RNA environment global | RNA/Protein |
| RNA family chains | A/1A: rRNA |
| RNA family global | rRNA |
| Volume | - |
| Hydrophobicity | - |
| Hydrophilicity | - |
| Buriedness | - |
| Don/acc character | - |
| SiteScore | - |
| D Score | - |
| Kd | — |
| Compound | CPF |
| Residue | . / 4056 |
| Chain | RRA / 1A |
| Non-redundant | True |
| Interacting RNA chains | A/1A |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | A/1A: rRNA |
| RNA family global | rRNA |
| Volume | 307.33 Å3 |
| Hydrophobicity | 0.149 |
| Hydrophilicity | 2.026 |
| Buriedness | 0.706 |
| Don/acc character | 0.332 |
| SiteScore | 1.102 |
| D Score | 0.635 |
| Kd | — |
| Compound | CPF |
| Residue | . / 3741 |
| Chain | UMC / 2A |
| Non-redundant | True |
| Interacting RNA chains | BB/2A |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | BB/2A: rRNA |
| RNA family global | rRNA |
| Volume | 273.37 Å3 |
| Hydrophobicity | 0.616 |
| Hydrophilicity | 1.339 |
| Buriedness | 0.698 |
| Don/acc character | 0.562 |
| SiteScore | 1.026 |
| D Score | 0.763 |
| Kd | — |