sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.500 Å
X-ray
2010-03-02
| Name: | Uncharacterized protein |
|---|---|
| ID: | Q6WRH7_BRABE |
| AC: | Q6WRH7 |
| Organism: | Branchiostoma belcheri tsingtauense |
| Reign: | Eukaryota |
| TaxID: | 155462 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 31.615 |
|---|---|
| Number of residues: | 24 |
| Including | |
| Standard Amino Acids: | 24 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.972 | 330.750 |
| % Hydrophobic | % Polar |
|---|---|
| 74.49 | 25.51 |
| According to VolSite | |
| HET Code: | GDP |
|---|---|
| Formula: | C10H12N5O11P2 |
| Molecular weight: | 440.177 g/mol |
| DrugBank ID: | DB04315 |
| Buried Surface Area: | 35.74 % |
| Polar Surface area: | 276.39 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 14 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 3 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -25.2019 | -8.20086 | 8.80321 |
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' | CG | PRO- 25 | 3.99 | 0 | Hydrophobic |
| C4' | CZ | PHE- 31 | 3.41 | 0 | Hydrophobic |
| C1' | CE1 | PHE- 31 | 3.26 | 0 | Hydrophobic |
| N2 | OG1 | THR- 54 | 3.47 | 153.33 | H-Bond (Ligand Donor) |
| DuAr | DuAr | PHE- 140 | 3.66 | 0 | Aromatic Face/Face |
| C2' | CE2 | PHE- 140 | 3.67 | 0 | Hydrophobic |
