Complex 9ynp
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 | Electron Microscopy |
| Experimental resolution | 3.06 |
| System mass | 476.06 kDa |
| Deposition year | 2025 |
| Molecule type | RNA/DNA/Protein |
| # RNA entities | 1 |
| Organism | Escherichia |
| RCSB PDB Entry | 9ynp |
| Reference | Anwar Avraz F., You Linlin, Degen David, Burns Katie J., Garza Michael J., Ebright Richard H., Del Valle Juan R.. 2026. Solid-Phase Synthesis and Biological Evaluation of Des-hydroxy Pseudouridimycin Analogs ACS Medicinal Chemistry Letters |
| Equivalence Class |
NR_all_04288.8
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 | PUM |
| Residue | . / 1601 |
| Chain | M / I |
| Non-redundant | True |
| Interacting RNA chains | I/I |
| RNA environment detailled | DNA, protein, ion |
| RNA environment global | RNA/DNA/Protein |
| RNA family chains | I/I: unknown |
| RNA family global | unknown |
| Volume | 622.20 Å3 |
| Hydrophobicity | 0.529 |
| Hydrophilicity | 1.084 |
| Buriedness | 0.816 |
| Don/acc character | 0.752 |
| SiteScore | 1.079 |
| D Score | 1.076 |
| Kd | — |