sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
2001-11-27
| Name: | Transthyretin |
|---|---|
| ID: | TTHY_RAT |
| AC: | P02767 |
| Organism: | Rattus norvegicus |
| Reign: | Eukaryota |
| TaxID: | 10116 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 7 % |
| B | 46 % |
| C | 7 % |
| D | 39 % |
| B-Factor: | 7.317 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.413 | 681.750 |
| % Hydrophobic | % Polar |
|---|---|
| 56.93 | 43.07 |
| According to VolSite | |
| HET Code: | FL8 |
|---|---|
| Formula: | C16H9Br2O4 |
| Molecular weight: | 425.048 g/mol |
| DrugBank ID: | DB01838 |
| Buried Surface Area: | 59.11 % |
| Polar Surface area: | 69.59 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 1 |
| X | Y | Z |
|---|---|---|
| 42.5333 | 91.504 | 42.056 |
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 | CD | LYS- 215 | 3.27 | 0 | Hydrophobic |
| C1' | CD1 | LEU- 217 | 4.31 | 0 | Hydrophobic |
| C3B | CG | LEU- 217 | 4.27 | 0 | Hydrophobic |
| C7 | CG2 | THR- 306 | 3.76 | 0 | Hydrophobic |
| C8 | CB | ALA- 308 | 3.68 | 0 | Hydrophobic |
| C2' | CB | ALA- 308 | 3.73 | 0 | Hydrophobic |
| C4' | CD2 | LEU- 310 | 4.41 | 0 | Hydrophobic |
| BR3 | CB | LEU- 310 | 4.08 | 0 | Hydrophobic |
| BR3 | CB | SER- 317 | 4.23 | 0 | Hydrophobic |
| O4' | OG | SER- 317 | 3.38 | 146.82 | H-Bond (Ligand Donor) |
| BR3 | CB | THR- 319 | 4.18 | 0 | Hydrophobic |
| C8 | CD1 | LEU- 617 | 3.83 | 0 | Hydrophobic |
| C1' | CD1 | LEU- 617 | 4.3 | 0 | Hydrophobic |
| BR5 | CB | ALA- 708 | 4.19 | 0 | Hydrophobic |
| C6' | CB | ALA- 708 | 3.48 | 0 | Hydrophobic |
| BR3 | CD2 | LEU- 710 | 4.39 | 0 | Hydrophobic |
| C4' | CD2 | LEU- 710 | 4.12 | 0 | Hydrophobic |
| BR5 | CB | LEU- 710 | 4.13 | 0 | Hydrophobic |
| BR5 | CB | SER- 717 | 4.23 | 0 | Hydrophobic |
| C6' | CG2 | THR- 719 | 4.07 | 0 | Hydrophobic |
| C3B | CG2 | THR- 719 | 4.24 | 0 | Hydrophobic |
| BR5 | CG2 | THR- 719 | 3.76 | 0 | Hydrophobic |
