Complex 4nyg
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 | 3.05 |
| System mass | 27.27 kDa |
| Deposition year | 2013 |
| Molecule type | RNA |
| # RNA entities | 1 |
| Organism | Escherichia |
| RCSB PDB Entry | 4nyg |
| Reference | Warner Katherine Deigan, Homan Philip, Weeks Kevin M., Smith Alison G., Abell Chris, Ferré-D’Amaré Adrian R.. 2014. Validating Fragment-Based Drug Discovery for Biological RNAs: Lead Fragments Bind and Remodel the TPP Riboswitch Specifically Chemistry & Biology |
| Equivalence Class |
NR_all_42241.5
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 | VIB |
| Residue | . / 101 |
| Chain | B / A |
| Non-redundant | False |
| Interacting RNA chains | A/A |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | A/A: riboswitch |
| RNA family global | riboswitch |
| Volume | 410.57 Å3 |
| Hydrophobicity | 0.564 |
| Hydrophilicity | 1.068 |
| Buriedness | 0.722 |
| Don/acc character | 1.555 |
| SiteScore | 1.166 |
| D Score | 1.025 |
| Kd | 1.5uM |