Complex 2a04
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 | 2.95 |
| System mass | 21.08 kDa |
| Deposition year | 2005 |
| Molecule type | RNA |
| # RNA entities | 1 |
| Organism | N/A |
| RCSB PDB Entry | 2a04 |
| Reference | Zhao Fang, Zhao Qiang, Blount Kenneth F., Han Qing, Tor Yitzhak, Hermann Thomas. 2005. Molecular Recognition of RNA by Neomycin and a Restricted Neomycin Derivative Angewandte Chemie International Edition |
| Equivalence Class |
NR_all_22842.2
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 | NMY |
| Residue | . / 17 |
| Chain | E / 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: rRNA, B/B: rRNA |
| RNA family global | rRNA |
| Volume | 59.34 Å3 |
| Hydrophobicity | 0.210 |
| Hydrophilicity | 0.861 |
| Buriedness | 0.554 |
| Don/acc character | 2.714 |
| SiteScore | 0.763 |
| D Score | 0.575 |
| Kd | — |
| Compound | NMY |
| Residue | . / 18 |
| Chain | F / A |
| Non-redundant | True |
| Interacting RNA chains | A/A |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | A/A: rRNA |
| RNA family global | rRNA |
| Volume | 42.53 Å3 |
| Hydrophobicity | 0.005 |
| Hydrophilicity | 0.657 |
| Buriedness | 0.409 |
| Don/acc character | 4.275 |
| SiteScore | 1.031 |
| D Score | 0.972 |
| Kd | — |
| Compound | NMY |
| Residue | . / 1 |
| Chain | H / C |
| Non-redundant | False |
| Interacting RNA chains | C/C, D/D |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | C/C: rRNA, D/D: rRNA |
| RNA family global | rRNA |
| Volume | 53.17 Å3 |
| Hydrophobicity | 0.091 |
| Hydrophilicity | 0.900 |
| Buriedness | 0.556 |
| Don/acc character | 3.344 |
| SiteScore | 0.708 |
| D Score | 0.501 |
| Kd | — |
| Compound | NMY |
| Residue | . / 17 |
| Chain | I / C |
| Non-redundant | False |
| Interacting RNA chains | C/C |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | C/C: rRNA |
| RNA family global | rRNA |
| Volume | 96.38 Å3 |
| Hydrophobicity | 0.010 |
| Hydrophilicity | 0.615 |
| Buriedness | 0.488 |
| Don/acc character | 3.338 |
| SiteScore | 1.091 |
| D Score | 1.032 |
| Kd | — |