Complex 8u60
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 | 3.30 |
| System mass | 37.44 kDa |
| Deposition year | 2023 |
| Molecule type | RNA |
| # RNA entities | 1 |
| Organism | N/A |
| RCSB PDB Entry | 8u60 |
| 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 | . / 105 |
| Chain | H / A |
| Non-redundant | False |
| 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 | 344.72 Å3 |
| Hydrophobicity | 0.535 |
| Hydrophilicity | 0.701 |
| Buriedness | 0.604 |
| Don/acc character | 3.205 |
| SiteScore | 1.152 |
| D Score | 1.074 |
| Kd | — |
| Compound | VK0 |
| Residue | . / 105 |
| Chain | M / B |
| Non-redundant | False |
| Interacting RNA chains | B/B |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | B/B: aptamer_rna |
| RNA family global | aptamer_rna |
| Volume | 270.63 Å3 |
| Hydrophobicity | 0.561 |
| Hydrophilicity | 0.843 |
| Buriedness | 0.588 |
| Don/acc character | 2.723 |
| SiteScore | 1.115 |
| D Score | 1.018 |
| Kd | — |
| Compound | VK0 |
| Residue | . / 105 |
| Chain | R / 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 | 306.30 Å3 |
| Hydrophobicity | 0.749 |
| Hydrophilicity | 0.716 |
| Buriedness | 0.587 |
| Don/acc character | 1.779 |
| SiteScore | 1.138 |
| D Score | 1.058 |
| Kd | — |