Complex 8hzd
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 | 1.87 |
| System mass | 24.22 kDa |
| Deposition year | 2023 |
| Molecule type | RNA |
| # RNA entities | 1 |
| Organism | N/A |
| RCSB PDB Entry | 8hzd |
| Reference | Huang Kaiyi, Song Qianqian, Fang Mengyue, Yao Deqiang, Shen Xin, Xu Xiaochen, Chen Xianjun, Zhu Linyong, Yang Yi, Ren Aiming. 2024. Structural basis of a small monomeric Clivia fluorogenic RNA with a large Stokes shift Nature Chemical Biology |
| Equivalence Class |
NR_all_04219.3
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 | O2I |
| Residue | . / 104 |
| Chain | F / 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 | 373.53 Å3 |
| Hydrophobicity | 0.815 |
| Hydrophilicity | 0.807 |
| Buriedness | 0.632 |
| Don/acc character | 3.161 |
| SiteScore | 1.151 |
| D Score | 1.056 |
| Kd | — |
| Compound | O2I |
| Residue | . / 105 |
| Chain | K / 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 | 322.42 Å3 |
| Hydrophobicity | 1.032 |
| Hydrophilicity | 0.866 |
| Buriedness | 0.664 |
| Don/acc character | 3.486 |
| SiteScore | 1.161 |
| D Score | 1.057 |
| Kd | — |