sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.900 Å
X-ray
2004-03-10
| Name: | Transthyretin |
|---|---|
| ID: | Q9PTT3_SPAAU |
| AC: | Q9PTT3 |
| Organism: | Sparus aurata |
| Reign: | Eukaryota |
| TaxID: | 8175 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 50 % |
| D | 50 % |
| B-Factor: | 12.809 |
|---|---|
| Number of residues: | 26 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.548 | 698.625 |
| % Hydrophobic | % Polar |
|---|---|
| 66.18 | 33.82 |
| According to VolSite | |
| HET Code: | T3 |
|---|---|
| Formula: | C15H12I3NO4 |
| Molecular weight: | 650.973 g/mol |
| DrugBank ID: | DB00279 |
| Buried Surface Area: | 49.28 % |
| Polar Surface area: | 97.23 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| -70.5872 | -24.8204 | -18.6652 |
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 |
| C2 | CG | LYS- 15 | 4.26 | 0 | Hydrophobic |
| I1 | CB | LYS- 15 | 4.3 | 0 | Hydrophobic |
| C12 | CG | LYS- 15 | 3.7 | 0 | Hydrophobic |
| C7 | CG | LYS- 15 | 3.89 | 0 | Hydrophobic |
| C7 | CG | LYS- 15 | 4.06 | 0 | Hydrophobic |
| O3 | NZ | LYS- 15 | 3.14 | 0 | Ionic (Protein Cationic) |
| I1 | CD1 | LEU- 17 | 4.44 | 0 | Hydrophobic |
| I3 | CD1 | LEU- 17 | 3.89 | 0 | Hydrophobic |
| C4 | CD1 | LEU- 17 | 3.9 | 0 | Hydrophobic |
| C8 | CD1 | LEU- 17 | 3.23 | 0 | Hydrophobic |
| N1 | OE2 | GLU- 54 | 3.23 | 165.93 | H-Bond (Ligand Donor) |
| N1 | OE2 | GLU- 54 | 3.23 | 0 | Ionic (Ligand Cationic) |
| I1 | CG2 | THR- 106 | 4.05 | 0 | Hydrophobic |
| I3 | CG2 | THR- 106 | 4.11 | 0 | Hydrophobic |
| C4 | CB | ALA- 108 | 4.28 | 0 | Hydrophobic |
| I1 | CB | ALA- 108 | 4.29 | 0 | Hydrophobic |
| I3 | CB | ALA- 108 | 4.21 | 0 | Hydrophobic |
| C10 | CB | ALA- 108 | 3.61 | 0 | Hydrophobic |
| O1 | O | LEU- 109 | 3.1 | 162.3 | H-Bond (Ligand Donor) |
| I2 | CB | LEU- 110 | 4.38 | 0 | Hydrophobic |
| I3 | CG2 | VAL- 121 | 3.54 | 0 | Hydrophobic |
