Complex 9j6p
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 | 2.49 |
| System mass | 15.30 kDa |
| Deposition year | 2024 |
| Molecule type | RNA |
| # RNA entities | 1 |
| Organism | N/A |
| RCSB PDB Entry | 9j6p |
| Reference | Nagasawa Ryosuke, Onizuka Kazumitsu, Kawamura Karen, Tsuzuki Kosuke, Murase Hirotaka, Komatsu Kaoru R., Miyashita Emi, Saito Hirohide, Kondo Jiro, Nagatsugi Fumi. 2025. Crystallographic analysis of G-clamp–RNA complex assisted by large scale RNA-binding profile Chemical Communications |
| Equivalence Class |
NR_all_08425.1
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 | A1L3Y |
| Residue | . / 101 |
| Chain | C / A |
| Non-redundant | True |
| Interacting RNA chains | B/B, A/A |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | A/A: synthetic construct, B/B: synthetic construct |
| RNA family global | synthetic construct |
| Volume | 457.91 Å3 |
| Hydrophobicity | 0.258 |
| Hydrophilicity | 0.941 |
| Buriedness | 0.640 |
| Don/acc character | 2.170 |
| SiteScore | 1.131 |
| D Score | 1.017 |
| Kd | — |
| Compound | A1L3Y |
| Residue | . / 101 |
| Chain | D / B |
| Non-redundant | True |
| Interacting RNA chains | B/B, A/A |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | A/A: synthetic construct, B/B: synthetic construct |
| RNA family global | synthetic construct |
| Volume | 79.23 Å3 |
| Hydrophobicity | 0.056 |
| Hydrophilicity | 1.252 |
| Buriedness | 0.559 |
| Don/acc character | 1.093 |
| SiteScore | 0.827 |
| D Score | 0.572 |
| Kd | — |