Complex 1q8n
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 | Solution NMR |
| Experimental resolution | N/A |
| System mass | 12.65 kDa |
| Deposition year | 2003 |
| Molecule type | RNA |
| # RNA entities | 1 |
| Organism | N/A |
| RCSB PDB Entry | 1q8n |
| Reference | Flinders Jeremy, DeFina Steven C., Brackett David M., Baugh Chris, Wilson Charles, Dieckmann Thorsten. 2004. Recognition of Planar and Nonplanar Ligands in the Malachite Green–RNA Aptamer Complex ChemBioChem |
| Molecular Dynamics Simulation | mmb-A01WO, mmb-A01WW, mmb-A01XF, mmb-A0227, mmb-A022H |
| Equivalence Class |
NR_all_93156.1
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 | MGR |
| Residue | . / 39 |
| Chain | B / A |
| Non-redundant | True |
| Interacting RNA chains | A/A |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | A/A: aptamer_rna |
| RNA family global | aptamer_rna |
| Volume | 670.22 Å3 |
| Hydrophobicity | 0.653 |
| Hydrophilicity | 1.138 |
| Buriedness | 0.723 |
| Don/acc character | 1.370 |
| SiteScore | 1.167 |
| D Score | 1.003 |
| Kd | 800nM |