Complex 5bs3
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 | 2.65 |
| System mass | 169.87 kDa |
| Deposition year | 2015 |
| Molecule type | RNA/DNA/Protein |
| # RNA entities | 1 |
| Organism | Staphylococcus |
| RCSB PDB Entry | 5bs3 |
| Reference | Singh Sheo B., Kaelin David E., Wu Jin, Miesel Lynn, Tan Christopher M., Black Todd, Nargund Ravi, Meinke Peter T., Olsen David B., Lagrutta Armando, Lu Jun, Patel Sangita, Rickert Keith W., Smith Robert F., Soisson Stephen, Sherer Edward, Joyce Leo A., Wei Changqing, Peng Xuanjia, Wang Xiu, Fukuda Hideyuki, Kishii Ryuta, Takei Masaya, Takano Hisashi, Shibasaki Mitsuhito, Yajima Masanobu, Nishimura Akinori, Shibata Takeshi, Fukuda Yasumichi. 2015. Tricyclic 1,5-naphthyridinone oxabicyclooctane-linked novel bacterial topoisomerase inhibitors as broad-spectrum antibacterial agents-SAR of left-hand-side moiety (Part-2) Bioorganic & Medicinal Chemistry Letters |
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 | WCP |
| Residue | . / 101 |
| Chain | I / F |
| Non-redundant | True |
| Interacting RNA chains | C/E, D/F |
| RNA environment detailled | protein |
| RNA environment global | RNA/Protein |
| RNA family chains | C/E: RNA/DNA_hybrid, D/F: RNA/DNA_hybrid |
| RNA family global | RNA/DNA_hybrid |
| Volume | 189.68 Å3 |
| Hydrophobicity | 3.100 |
| Hydrophilicity | 0.797 |
| Buriedness | 0.858 |
| Don/acc character | 0.465 |
| SiteScore | 0.944 |
| D Score | 0.926 |
| Kd | — |