Complex 3dil
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 | 1.90 |
| System mass | 58.37 kDa |
| Deposition year | 2008 |
| Molecule type | RNA |
| # RNA entities | 1 |
| Organism | Thermotoga |
| RCSB PDB Entry | 3dil |
| Reference | Serganov Alexander, Huang Lili, Patel Dinshaw J.. 2008. Structural insights into amino acid binding and gene control by a lysine riboswitch Nature |
| Equivalence Class |
NR_all_29848.3
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 | 1PE |
| Residue | . / 250 |
| Chain | JA / A |
| Non-redundant | True |
| Interacting RNA chains | A/A |
| RNA environment detailled | other |
| RNA environment global | RNA/Other |
| RNA family chains | A/A: riboswitch |
| RNA family global | riboswitch |
| Volume | 248.33 Å3 |
| Hydrophobicity | 0.098 |
| Hydrophilicity | 1.114 |
| Buriedness | 0.728 |
| Don/acc character | 3.178 |
| SiteScore | 0.781 |
| D Score | 0.514 |
| Kd | — |
| Compound | 1PE |
| Residue | . / 251 |
| Chain | KA / A |
| Non-redundant | False |
| Interacting RNA chains | A/A |
| RNA environment detailled | ion, other |
| RNA environment global | RNA/Other |
| RNA family chains | A/A: riboswitch |
| RNA family global | riboswitch |
| Volume | 164.30 Å3 |
| Hydrophobicity | 0.078 |
| Hydrophilicity | 0.963 |
| Buriedness | 0.710 |
| Don/acc character | 3.991 |
| SiteScore | 0.694 |
| D Score | 0.438 |
| Kd | — |
| Compound | 1PE |
| Residue | . / 252 |
| Chain | LA / A |
| Non-redundant | True |
| Interacting RNA chains | A/A |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | A/A: riboswitch |
| RNA family global | riboswitch |
| Volume | - |
| Hydrophobicity | - |
| Hydrophilicity | - |
| Buriedness | - |
| Don/acc character | - |
| SiteScore | - |
| D Score | - |
| Kd | — |