sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.580 Å
X-ray
2014-11-27
| Name: | Uncharacterized protein |
|---|---|
| ID: | E0RR11_SPITD |
| AC: | E0RR11 |
| Organism: | Spirochaeta thermophila |
| Reign: | Bacteria |
| TaxID: | 665571 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 76.097 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.512 | 249.750 |
| % Hydrophobic | % Polar |
|---|---|
| 62.16 | 37.84 |
| According to VolSite | |
| HET Code: | CMP |
|---|---|
| Formula: | C10H11N5O6P |
| Molecular weight: | 328.198 g/mol |
| DrugBank ID: | DB02527 |
| Buried Surface Area: | 87.47 % |
| Polar Surface area: | 167.48 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 10 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 1 |
| X | Y | Z |
|---|---|---|
| -56.0045 | 7.27682 | -28.3527 |
Image generated by PoseView
Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand
| Ligand | Protein | Interaction | |||
|---|---|---|---|---|---|
| Atom | Atom | Residue | Distance (Å) | Angle (°) | Type |
| C5' | CG2 | ILE- 329 | 4.14 | 0 | Hydrophobic |
| C1' | CG1 | VAL- 348 | 4.14 | 0 | Hydrophobic |
| C1' | CB | PHE- 366 | 4.21 | 0 | Hydrophobic |
| O3' | N | GLY- 367 | 3.35 | 120.87 | H-Bond (Protein Donor) |
| O2' | N | GLY- 367 | 2.82 | 148.85 | H-Bond (Protein Donor) |
| O2' | OE2 | GLU- 368 | 3.2 | 138.82 | H-Bond (Ligand Donor) |
| O3' | N | MET- 369 | 3.27 | 149.84 | H-Bond (Protein Donor) |
| C2' | SD | MET- 369 | 3.54 | 0 | Hydrophobic |
| O2P | N | ALA- 370 | 2.91 | 144.1 | H-Bond (Protein Donor) |
| O1P | N | THR- 378 | 3.07 | 170.33 | H-Bond (Protein Donor) |
| O1P | OG1 | THR- 378 | 3.24 | 164.04 | H-Bond (Protein Donor) |
| C5' | CB | ALA- 379 | 4.21 | 0 | Hydrophobic |
| C5' | CG2 | VAL- 381 | 4.2 | 0 | Hydrophobic |
| N6 | OE2 | GLU- 421 | 2.94 | 131.55 | H-Bond (Ligand Donor) |
