Complex 9hrd
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 | 2.50 |
| System mass | 93.37 kDa |
| Deposition year | 2024 |
| Molecule type | RNA |
| # RNA entities | 1 |
| Organism | N/A |
| RCSB PDB Entry | 9hrd |
| Reference | Stafflinger Helena, Neißner Konstantin, Bartsch Saskia, Pichler Alexander K, Bartosik Karolina, Dhamotharan Karthikeyan, Abele Rupert, Duchardt-Ferner Elke, Micura Ronald, Schindelin Hermann, Wöhnert Jens. 2025. Crystal structure of the class V GTP-binding RNA aptamer bound to its ligand: GTP recognition by a topologically complex intermolecular G-quadruplex Nucleic Acids Research |
| Equivalence Class |
NR_all_44054.1
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 | GTP |
| Residue | . / 107 |
| Chain | K / A |
| Non-redundant | True |
| Interacting RNA chains | A/A, B/B |
| RNA environment detailled | ion, other |
| RNA environment global | RNA/Other |
| RNA family chains | A/A: aptamer_rna, B/B: aptamer_rna |
| RNA family global | aptamer_rna |
| Volume | 267.88 Å3 |
| Hydrophobicity | 0.357 |
| Hydrophilicity | 1.121 |
| Buriedness | 0.736 |
| Don/acc character | 1.087 |
| SiteScore | 0.929 |
| D Score | 0.700 |
| Kd | — |
| Compound | GTP |
| Residue | . / 107 |
| Chain | R / B |
| Non-redundant | False |
| Interacting RNA chains | A/A, B/B |
| RNA environment detailled | ion, other |
| RNA environment global | RNA/Other |
| RNA family chains | A/A: aptamer_rna, B/B: aptamer_rna |
| RNA family global | aptamer_rna |
| Volume | 503.18 Å3 |
| Hydrophobicity | 0.203 |
| Hydrophilicity | 1.273 |
| Buriedness | 0.702 |
| Don/acc character | 1.704 |
| SiteScore | 1.126 |
| D Score | 0.913 |
| Kd | — |
| Compound | GTP |
| Residue | . / 107 |
| Chain | Y / 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 | 66.54 Å3 |
| Hydrophobicity | 0.131 |
| Hydrophilicity | 1.435 |
| Buriedness | 0.688 |
| Don/acc character | 0.798 |
| SiteScore | 0.762 |
| D Score | 0.396 |
| Kd | — |
| Compound | GTP |
| Residue | . / 107 |
| Chain | FA / D |
| Non-redundant | False |
| Interacting RNA chains | D/D |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | D/D: aptamer_rna |
| RNA family global | aptamer_rna |
| Volume | - |
| Hydrophobicity | - |
| Hydrophilicity | - |
| Buriedness | - |
| Don/acc character | - |
| SiteScore | - |
| D Score | - |
| Kd | — |