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 | 56 % |
| D | 44 % |
| B-Factor: | 13.894 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.565 | 472.500 |
| % Hydrophobic | % Polar |
|---|---|
| 70.00 | 30.00 |
| According to VolSite | |
| HET Code: | T44 |
|---|---|
| Formula: | C15H10I4NO4 |
| Molecular weight: | 775.862 g/mol |
| DrugBank ID: | DB00451 |
| Buried Surface Area: | 48.58 % |
| Polar Surface area: | 100.06 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 1 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 2 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| -71.1927 | -24.7108 | -18.1308 |
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 |
| C4 | CG | LYS- 15 | 4.3 | 0 | Hydrophobic |
| C2' | CG | LYS- 15 | 3.73 | 0 | Hydrophobic |
| C6' | CG | LYS- 15 | 3.97 | 0 | Hydrophobic |
| C1 | CD | LYS- 15 | 3.39 | 0 | Hydrophobic |
| C4 | CG | LYS- 15 | 3.72 | 0 | Hydrophobic |
| O9 | NZ | LYS- 15 | 2.96 | 144.27 | H-Bond (Protein Donor) |
| O9 | NZ | LYS- 15 | 2.96 | 0 | Ionic (Protein Cationic) |
| I3 | CD1 | LEU- 17 | 4.38 | 0 | Hydrophobic |
| I3' | CD1 | LEU- 17 | 3.41 | 0 | Hydrophobic |
| I5' | CD1 | LEU- 17 | 3.62 | 0 | Hydrophobic |
| C6' | CD1 | LEU- 17 | 3.5 | 0 | Hydrophobic |
| C3' | CD1 | LEU- 17 | 3.48 | 0 | Hydrophobic |
| C5' | CD1 | LEU- 17 | 3.53 | 0 | Hydrophobic |
| N8 | OE2 | GLU- 54 | 3.75 | 0 | Ionic (Ligand Cationic) |
| I3 | CG2 | THR- 106 | 4.13 | 0 | Hydrophobic |
| I5 | CG2 | THR- 106 | 4.15 | 0 | Hydrophobic |
| I3' | CB | ALA- 108 | 3.9 | 0 | Hydrophobic |
| I5' | CB | ALA- 108 | 3.69 | 0 | Hydrophobic |
| C3' | CB | ALA- 108 | 3.82 | 0 | Hydrophobic |
| C5' | CB | ALA- 108 | 3.76 | 0 | Hydrophobic |
| I3' | CB | LEU- 110 | 4.08 | 0 | Hydrophobic |
| I5' | CB | LEU- 110 | 4.09 | 0 | Hydrophobic |
| I3 | CG2 | VAL- 121 | 4.15 | 0 | Hydrophobic |
