Complex 8u5k
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 | 2.80 |
| System mass | 37.36 kDa |
| Deposition year | 2023 |
| Molecule type | RNA |
| # RNA entities | 1 |
| Organism | N/A |
| RCSB PDB Entry | 8u5k |
| Reference | Lu Xiaocen, Passalacqua Luiz F M, Nodwell Matthew, Kong Kristen Y S, Caballero-García Guillermo, Dolgosheina Elena V, Ferré-D’Amaré Adrian R, Britton Robert, Unrau Peter J. 2024. Symmetry breaking of fluorophore binding to a G-quadruplex generates an RNA aptamer with picomolar KD Nucleic Acids Research |
| Equivalence Class |
NR_all_82829.3
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 | VK0 |
| Residue | . / 104 |
| Chain | G / A |
| Non-redundant | True |
| Interacting RNA chains | A/A |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | A/A: aptamer_rna |
| RNA family global | aptamer_rna |
| Volume | 307.67 Å3 |
| Hydrophobicity | 0.513 |
| Hydrophilicity | 0.717 |
| Buriedness | 0.589 |
| Don/acc character | 4.093 |
| SiteScore | 1.139 |
| D Score | 1.060 |
| Kd | — |
| Compound | VK0 |
| Residue | . / 103 |
| Chain | J / B |
| Non-redundant | False |
| Interacting RNA chains | B/B |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | B/B: aptamer_rna |
| RNA family global | aptamer_rna |
| Volume | 321.05 Å3 |
| Hydrophobicity | 0.521 |
| Hydrophilicity | 0.687 |
| Buriedness | 0.603 |
| Don/acc character | 4.483 |
| SiteScore | 1.155 |
| D Score | 1.078 |
| Kd | — |
| Compound | VK0 |
| Residue | . / 104 |
| Chain | N / C |
| Non-redundant | False |
| Interacting RNA chains | C/C |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | C/C: aptamer_rna |
| RNA family global | aptamer_rna |
| Volume | 317.96 Å3 |
| Hydrophobicity | 0.499 |
| Hydrophilicity | 0.746 |
| Buriedness | 0.615 |
| Don/acc character | 3.238 |
| SiteScore | 1.151 |
| D Score | 1.066 |
| Kd | — |