Complex 3d2v
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 | 2.00 |
| System mass | 51.00 kDa |
| Deposition year | 2008 |
| Molecule type | RNA |
| # RNA entities | 1 |
| Organism | Arabidopsis |
| RCSB PDB Entry | 3d2v |
| Reference | Thore Stéphane, Frick Christian, Ban Nenad. 2008. Structural Basis of Thiamine Pyrophosphate Analogues Binding to the Eukaryotic Riboswitch Journal of the American Chemical Society |
| Equivalence Class |
NR_all_27756.3
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 | PYI |
| Residue | . / 84 |
| Chain | I / A |
| Non-redundant | True |
| Interacting RNA chains | A/A |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | A/A: riboswitch |
| RNA family global | riboswitch |
| Volume | 417.77 Å3 |
| Hydrophobicity | 0.781 |
| Hydrophilicity | 0.939 |
| Buriedness | 0.782 |
| Don/acc character | 1.959 |
| SiteScore | 1.088 |
| D Score | 0.927 |
| Kd | — |
| Compound | PYI |
| Residue | . / 82 |
| Chain | N / B |
| Non-redundant | False |
| Interacting RNA chains | B/B |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | B/B: riboswitch |
| RNA family global | riboswitch |
| Volume | 752.20 Å3 |
| Hydrophobicity | 0.332 |
| Hydrophilicity | 1.156 |
| Buriedness | 0.736 |
| Don/acc character | 1.492 |
| SiteScore | 1.175 |
| D Score | 1.005 |
| Kd | — |