sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.790 Å
X-ray
2010-12-22
| 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: | 13.336 |
|---|---|
| Number of residues: | 38 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 2 |
| Cofactors: | FAD |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 1.413 | 877.500 |
| % Hydrophobic | % Polar |
|---|---|
| 48.08 | 51.92 |
| According to VolSite | |
| HET Code: | TRK |
|---|---|
| Formula: | C22H26NO6 |
| Molecular weight: | 400.445 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 60.38 % |
| Polar Surface area: | 104.76 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 0 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 5.97731 | -9.64428 | 72.9211 |
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 |
| C13 | CZ | TYR- 64 | 4.35 | 0 | Hydrophobic |
| C15 | CZ | TYR- 64 | 3.94 | 0 | Hydrophobic |
| C20 | CB | ALA- 121 | 4.41 | 0 | Hydrophobic |
| C18 | SG | CYS- 122 | 4.06 | 0 | Hydrophobic |
| C20 | CG2 | VAL- 266 | 4.28 | 0 | Hydrophobic |
| N | O | THR- 334 | 2.81 | 161.56 | H-Bond (Ligand Donor) |
| C13 | CG1 | ILE- 339 | 3.56 | 0 | Hydrophobic |
| C3 | CB | ALA- 373 | 3.6 | 0 | Hydrophobic |
| C20 | CD1 | ILE- 375 | 4.34 | 0 | Hydrophobic |
| C15 | CG1 | VAL- 401 | 3.89 | 0 | Hydrophobic |
| C2 | CG1 | VAL- 401 | 4.05 | 0 | Hydrophobic |
| C13 | CG2 | VAL- 403 | 3.73 | 0 | Hydrophobic |
| C2 | CG2 | VAL- 403 | 4.17 | 0 | Hydrophobic |
| O6 | OH | TYR- 447 | 2.55 | 131.64 | H-Bond (Protein Donor) |
| C15 | CE1 | TYR- 447 | 3.72 | 0 | Hydrophobic |
| C16 | C6 | FAD- 600 | 3.4 | 0 | Hydrophobic |
| O2 | MG | MG- 800 | 2.06 | 0 | Metal Acceptor |
| O4 | MG | MG- 800 | 2.08 | 0 | Metal Acceptor |
