sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.500 Å
X-ray
2001-04-06
| Name: | Transthyretin |
|---|---|
| ID: | TTHY_RAT |
| AC: | P02767 |
| Organism: | Rattus norvegicus |
| Reign: | Eukaryota |
| TaxID: | 10116 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 50 % |
| C | 4 % |
| D | 46 % |
| B-Factor: | 9.649 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.676 | 1083.375 |
| % Hydrophobic | % Polar |
|---|---|
| 57.94 | 42.06 |
| According to VolSite | |
| HET Code: | T44 |
|---|---|
| Formula: | C15H10I4NO4 |
| Molecular weight: | 775.862 g/mol |
| DrugBank ID: | DB00451 |
| Buried Surface Area: | 53.5 % |
| 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 |
|---|---|---|
| 43.485 | 93.5772 | 42.6356 |
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 |
| O10 | NZ | LYS- 15 | 3.37 | 147.93 | H-Bond (Protein Donor) |
| O10 | NZ | LYS- 15 | 3.37 | 0 | Ionic (Protein Cationic) |
| I5 | CD | LYS- 15 | 4.47 | 0 | Hydrophobic |
| C2 | CG | LYS- 15 | 3.61 | 0 | Hydrophobic |
| C1 | CD | LYS- 15 | 3.61 | 0 | Hydrophobic |
| C4 | CD | LYS- 15 | 3.64 | 0 | Hydrophobic |
| C5' | CD1 | LEU- 17 | 4.49 | 0 | Hydrophobic |
| I3 | CD1 | LEU- 17 | 4.03 | 0 | Hydrophobic |
| I5 | CD1 | LEU- 17 | 4.15 | 0 | Hydrophobic |
| C1' | CD1 | LEU- 17 | 4.1 | 0 | Hydrophobic |
| C7 | CG | GLU- 54 | 4.44 | 0 | Hydrophobic |
| N8 | OE2 | GLU- 54 | 3.41 | 166.2 | H-Bond (Ligand Donor) |
| N8 | OE2 | GLU- 54 | 3.41 | 0 | Ionic (Ligand Cationic) |
| N8 | OE1 | GLU- 54 | 3.58 | 0 | Ionic (Ligand Cationic) |
| I5 | CG2 | THR- 106 | 4.16 | 0 | Hydrophobic |
| I3 | CB | ALA- 108 | 4.22 | 0 | Hydrophobic |
| I3' | CB | ALA- 108 | 3.54 | 0 | Hydrophobic |
| I5 | CB | ALA- 108 | 3.74 | 0 | Hydrophobic |
| I5' | CB | ALA- 108 | 3.3 | 0 | Hydrophobic |
| C2' | CB | ALA- 108 | 3.28 | 0 | Hydrophobic |
| C6' | CB | ALA- 108 | 3.79 | 0 | Hydrophobic |
| C4' | CD2 | LEU- 110 | 4.24 | 0 | Hydrophobic |
| I3' | CB | LEU- 110 | 4.14 | 0 | Hydrophobic |
| I5' | CB | LEU- 110 | 4.03 | 0 | Hydrophobic |
| C3' | CG2 | THR- 119 | 4.25 | 0 | Hydrophobic |
| I3' | CG2 | THR- 119 | 3.75 | 0 | Hydrophobic |
| I3 | CG2 | VAL- 121 | 4.3 | 0 | Hydrophobic |
| I5 | CG2 | VAL- 121 | 4.45 | 0 | Hydrophobic |
