Complex 6o97
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 | 2.75 |
| System mass | 4575.02 kDa |
| Deposition year | 2019 |
| Molecule type | RNA/Protein |
| # RNA entities | 1 |
| Organism | Thermus |
| RCSB PDB Entry | 6o97 |
| Reference | Matsushita Takahiko, Sati Girish C., Kondasinghe Nuwan, Pirrone Michael G., Kato Takayuki, Waduge Prabuddha, Kumar Harshitha Santhosh, Sanchon Adrian Cortes, Dobosz-Bartoszek Malgorzata, Shcherbakov Dimitri, Juhas Mario, Hobbie Sven N., Schrepfer Thomas, Chow Christine S., Polikanov Yury S., Schacht Jochen, Vasella Andrea, Böttger Erik C., Crich David. 2019. Design, Multigram Synthesis, and in Vitro and in Vivo Evaluation of Propylamycin: A Semisynthetic 4,5-Deoxystreptamine Class Aminoglycoside for the Treatment of Drug-Resistant Enterobacteriaceae and Other Gram-Negative Pathogens Journal of the American Chemical Society |
| Equivalence Class |
NR_all_65795.87,
NR_all_97519.80
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 | LUJ |
| Residue | . / 4099 |
| Chain | OTA / 1A |
| 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 | LUJ |
| Residue | . / 4100 |
| Chain | PTA / 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 | 263.08 Å3 |
| Hydrophobicity | 0.020 |
| Hydrophilicity | 1.519 |
| Buriedness | 0.595 |
| Don/acc character | 0.757 |
| SiteScore | 1.081 |
| D Score | 0.802 |
| Kd | — |
| Compound | LUJ |
| Residue | . / 1832 |
| Chain | DKB / 1a |
| Non-redundant | True |
| Interacting RNA chains | FA/1a |
| RNA environment detailled | protein, ion |
| RNA environment global | RNA/Protein |
| RNA family chains | FA/1a: rRNA |
| RNA family global | rRNA |
| Volume | 374.21 Å3 |
| Hydrophobicity | 0.222 |
| Hydrophilicity | 1.297 |
| Buriedness | 0.713 |
| Don/acc character | 0.911 |
| SiteScore | 1.010 |
| D Score | 0.945 |
| Kd | — |
| Compound | LUJ |
| Residue | . / 3851 |
| Chain | QSC / 2A |
| Non-redundant | True |
| Interacting RNA chains | EB/2A |
| RNA environment detailled | protein, ion |
| RNA environment global | RNA/Protein |
| RNA family chains | EB/2A: rRNA |
| RNA family global | rRNA |
| Volume | - |
| Hydrophobicity | - |
| Hydrophilicity | - |
| Buriedness | - |
| Don/acc character | - |
| SiteScore | - |
| D Score | - |
| Kd | — |
| Compound | LUJ |
| Residue | . / 3852 |
| Chain | RSC / 2A |
| Non-redundant | True |
| Interacting RNA chains | EB/2A |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | EB/2A: rRNA |
| RNA family global | rRNA |
| Volume | 271.31 Å3 |
| Hydrophobicity | 0.046 |
| Hydrophilicity | 1.374 |
| Buriedness | 0.611 |
| Don/acc character | 1.138 |
| SiteScore | 1.092 |
| D Score | 0.858 |
| Kd | — |
| Compound | LUJ |
| Residue | . / 3232 |
| Chain | WED / 2a |
| Non-redundant | True |
| Interacting RNA chains | JC/2a |
| RNA environment detailled | protein, ion |
| RNA environment global | RNA/Protein |
| RNA family chains | JC/2a: rRNA |
| RNA family global | rRNA |
| Volume | 786.84 Å3 |
| Hydrophobicity | 0.044 |
| Hydrophilicity | 1.447 |
| Buriedness | 0.680 |
| Don/acc character | 1.160 |
| SiteScore | 0.988 |
| D Score | 0.876 |
| Kd | — |