sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.300 Å
X-ray
2013-09-17
| Name: | Obelin |
|---|---|
| ID: | OBL_OBELO |
| AC: | Q27709 |
| Organism: | Obelia longissima |
| Reign: | Eukaryota |
| TaxID: | 32570 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 10.056 |
|---|---|
| Number of residues: | 45 |
| Including | |
| Standard Amino Acids: | 44 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.575 | 347.625 |
| % Hydrophobic | % Polar |
|---|---|
| 71.84 | 28.16 |
| According to VolSite | |
| HET Code: | CEI |
|---|---|
| Formula: | C25H21N3O3 |
| Molecular weight: | 411.453 g/mol |
| DrugBank ID: | DB04049 |
| Buried Surface Area: | 75.97 % |
| Polar Surface area: | 95.34 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 3 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 13.9935 | 25.7576 | 18.4895 |
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 |
| O25 | ND1 | HIS- 22 | 2.78 | 157.74 | H-Bond (Ligand Donor) |
| C19 | CE | MET- 25 | 4.03 | 0 | Hydrophobic |
| C22 | CB | MET- 25 | 3.5 | 0 | Hydrophobic |
| C23 | CG | MET- 25 | 3.79 | 0 | Hydrophobic |
| C28 | CE | MET- 25 | 3.78 | 0 | Hydrophobic |
| C21 | CD1 | LEU- 29 | 3.65 | 0 | Hydrophobic |
| C26 | CB | ALA- 46 | 3.93 | 0 | Hydrophobic |
| C26 | CG1 | ILE- 50 | 4.09 | 0 | Hydrophobic |
| C28 | CD1 | ILE- 50 | 3.78 | 0 | Hydrophobic |
| C23 | CZ2 | TRP- 92 | 3.34 | 0 | Hydrophobic |
| C10 | CG2 | VAL- 118 | 4.07 | 0 | Hydrophobic |
| C12 | CG2 | VAL- 118 | 3.54 | 0 | Hydrophobic |
| C16 | CG1 | VAL- 118 | 3.78 | 0 | Hydrophobic |
| C10 | CD1 | ILE- 141 | 3.77 | 0 | Hydrophobic |
| C16 | CD1 | ILE- 141 | 4.35 | 0 | Hydrophobic |
| C32 | CG2 | ILE- 141 | 3.53 | 0 | Hydrophobic |
| C30 | CB | SER- 142 | 4.43 | 0 | Hydrophobic |
| C15 | CE | MET- 171 | 3.85 | 0 | Hydrophobic |
| N4 | NE2 | HIS- 175 | 3.04 | 167.91 | H-Bond (Protein Donor) |
| DuAr | DuAr | HIS- 175 | 3.74 | 0 | Aromatic Face/Face |
| C14 | CB | HIS- 175 | 3.7 | 0 | Hydrophobic |
| C24 | CE3 | TRP- 179 | 3.39 | 0 | Hydrophobic |
| O33 | OH | TYR- 190 | 2.57 | 168.33 | H-Bond (Protein Donor) |
| N1 | O | HOH- 301 | 2.91 | 162.23 | H-Bond (Ligand Donor) |
