sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.670 Å
X-ray
2010-12-23
| Name: | TamL |
|---|---|
| ID: | D3Y1I2_9ACTN |
| AC: | D3Y1I2 |
| Organism: | Streptomyces sp. 307-9 |
| Reign: | Bacteria |
| TaxID: | 529089 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 13.668 |
|---|---|
| Number of residues: | 37 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 2 |
| Cofactors: | FAD |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 1.477 | 897.750 |
| % Hydrophobic | % Polar |
|---|---|
| 52.26 | 47.74 |
| According to VolSite | |
| HET Code: | TIR |
|---|---|
| Formula: | C22H28NO6 |
| Molecular weight: | 402.461 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 57.53 % |
| Polar Surface area: | 107.92 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 0 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 29.6149 | -24.1261 | 20.8618 |
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 |
| C15 | CZ | TYR- 64 | 4.06 | 0 | Hydrophobic |
| C21 | CZ | TYR- 64 | 4.33 | 0 | Hydrophobic |
| C12 | SG | CYS- 122 | 3.92 | 0 | Hydrophobic |
| C19 | CG2 | VAL- 266 | 4.33 | 0 | Hydrophobic |
| N | O | THR- 334 | 2.8 | 168.72 | H-Bond (Ligand Donor) |
| C21 | CG1 | ILE- 339 | 3.52 | 0 | Hydrophobic |
| C20 | CB | ALA- 373 | 3.48 | 0 | Hydrophobic |
| C19 | CD1 | ILE- 375 | 4.12 | 0 | Hydrophobic |
| C15 | CG1 | VAL- 401 | 3.94 | 0 | Hydrophobic |
| C9 | CG1 | VAL- 401 | 4.17 | 0 | Hydrophobic |
| C21 | CG1 | VAL- 403 | 3.87 | 0 | Hydrophobic |
| C9 | CG1 | VAL- 403 | 4.31 | 0 | Hydrophobic |
| C15 | CE1 | TYR- 447 | 3.82 | 0 | Hydrophobic |
| C16 | CZ | TYR- 447 | 4.35 | 0 | Hydrophobic |
| C13 | C6 | FAD- 600 | 3.43 | 0 | Hydrophobic |
| O5 | MG | MG- 800 | 2.19 | 0 | Metal Acceptor |
| O6 | MG | MG- 800 | 2.09 | 0 | Metal Acceptor |
