Complex 6yml
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 | 2.17 |
| System mass | 23.70 kDa |
| Deposition year | 2020 |
| Molecule type | RNA |
| # RNA entities | 1 |
| Organism | Roseobacter |
| RCSB PDB Entry | 6yml |
| Reference | Huang Lin, Liao Ting-Wei, Wang Jia, Ha Taekjip, Lilley David M J. 2020. Crystal structure and ligand-induced folding of the SAM/SAH riboswitch Nucleic Acids Research |
| Equivalence Class |
NR_all_57046.3
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 | AMP |
| Residue | . / 101 |
| Chain | E / A |
| Non-redundant | False |
| Interacting RNA chains | A/A, B/B |
| RNA environment detailled | other |
| RNA environment global | RNA/Other |
| RNA family chains | A/A: riboswitch, B/B: riboswitch |
| RNA family global | riboswitch |
| Volume | 31.21 Å3 |
| Hydrophobicity | 0.552 |
| Hydrophilicity | 0.909 |
| Buriedness | 0.672 |
| Don/acc character | 1.193 |
| SiteScore | 0.529 |
| D Score | 0.240 |
| Kd | — |
| Compound | DSH |
| Residue | . / 102 |
| Chain | F / A |
| Non-redundant | False |
| Interacting RNA chains | A/A, B/B |
| RNA environment detailled | other |
| RNA environment global | RNA/Other |
| RNA family chains | A/A: riboswitch, B/B: riboswitch |
| RNA family global | riboswitch |
| Volume | 359.46 Å3 |
| Hydrophobicity | 0.401 |
| Hydrophilicity | 0.987 |
| Buriedness | 0.663 |
| Don/acc character | 2.252 |
| SiteScore | 1.137 |
| D Score | 1.016 |
| Kd | — |
| Compound | DSH |
| Residue | . / 101 |
| Chain | H / C |
| Non-redundant | False |
| Interacting RNA chains | D/D, C/C |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | C/C: riboswitch, D/D: riboswitch |
| RNA family global | riboswitch |
| Volume | 409.20 Å3 |
| Hydrophobicity | 0.353 |
| Hydrophilicity | 0.986 |
| Buriedness | 0.622 |
| Don/acc character | 1.555 |
| SiteScore | 1.110 |
| D Score | 0.992 |
| Kd | — |