sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.170 Å
X-ray
2004-03-05
| 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: | 8.939 |
|---|---|
| Number of residues: | 40 |
| Including | |
| Standard Amino Acids: | 39 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.477 | 401.625 |
| % Hydrophobic | % Polar |
|---|---|
| 73.95 | 26.05 |
| According to VolSite | |
| HET Code: | CZH |
|---|---|
| Formula: | C26H22N3O5 |
| Molecular weight: | 456.470 g/mol |
| DrugBank ID: | DB02241 |
| Buried Surface Area: | 79.95 % |
| Polar Surface area: | 116.56 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 4 |
| Rings: | 5 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 6.35812 | 4.86797 | 33.3172 |
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 | 2.73 | 167.38 | H-Bond (Ligand Donor) |
| C19 | CE | MET- 25 | 3.59 | 0 | Hydrophobic |
| C22 | CB | MET- 25 | 3.3 | 0 | Hydrophobic |
| C23 | CG | MET- 25 | 3.58 | 0 | Hydrophobic |
| C21 | CD1 | LEU- 29 | 3.88 | 0 | Hydrophobic |
| C32 | CD2 | LEU- 29 | 3.97 | 0 | Hydrophobic |
| C31 | CG2 | ILE- 42 | 3.98 | 0 | Hydrophobic |
| C29 | CG | LYS- 45 | 4.34 | 0 | Hydrophobic |
| C31 | CD | LYS- 45 | 3.82 | 0 | Hydrophobic |
| C29 | CB | ALA- 46 | 4.14 | 0 | Hydrophobic |
| C28 | CD1 | ILE- 50 | 3.52 | 0 | Hydrophobic |
| C23 | CZ2 | TRP- 92 | 3.27 | 0 | Hydrophobic |
| C15 | CD1 | ILE- 111 | 3.86 | 0 | Hydrophobic |
| C10 | CZ2 | TRP- 114 | 3.79 | 0 | Hydrophobic |
| C16 | CB | TRP- 114 | 4.41 | 0 | Hydrophobic |
| C11 | CG2 | VAL- 118 | 4.08 | 0 | Hydrophobic |
| N1 | OH | TYR- 138 | 2.73 | 150.97 | H-Bond (Protein Donor) |
| C10 | CZ | TYR- 138 | 3.91 | 0 | Hydrophobic |
| C26 | CB | SER- 142 | 4.39 | 0 | Hydrophobic |
| C26 | CD1 | ILE- 144 | 4.34 | 0 | Hydrophobic |
| C13 | CG | MET- 171 | 4.04 | 0 | Hydrophobic |
| O18 | NE1 | TRP- 179 | 3.28 | 140.34 | H-Bond (Protein Donor) |
| O33 | OH | TYR- 190 | 3.22 | 150.11 | H-Bond (Protein Donor) |
| O34 | OH | TYR- 190 | 2.55 | 139.85 | H-Bond (Protein Donor) |
