sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
3.000 Å
X-ray
2001-04-02
| Name: | Transthyretin |
|---|---|
| ID: | TTHY_HUMAN |
| AC: | P02766 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 8 % |
| B | 50 % |
| C | 6 % |
| D | 36 % |
| B-Factor: | 13.465 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.303 | 867.375 |
| % Hydrophobic | % Polar |
|---|---|
| 55.64 | 44.36 |
| According to VolSite | |
| HET Code: | T44 |
|---|---|
| Formula: | C15H10I4NO4 |
| Molecular weight: | 775.862 g/mol |
| DrugBank ID: | DB00451 |
| Buried Surface Area: | 63.58 % |
| 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 |
|---|---|---|
| 17.0007 | -45.8972 | 42.0842 |
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 | CD | LYS- 15 | 3.85 | 0 | Hydrophobic |
| C7 | CD | LYS- 15 | 4.19 | 0 | Hydrophobic |
| O9 | NZ | LYS- 15 | 3.11 | 158.19 | H-Bond (Protein Donor) |
| O9 | NZ | LYS- 15 | 3.12 | 121.96 | H-Bond (Protein Donor) |
| O9 | NZ | LYS- 15 | 3.11 | 0 | Ionic (Protein Cationic) |
| O9 | NZ | LYS- 15 | 3.12 | 0 | Ionic (Protein Cationic) |
| O10 | NZ | LYS- 15 | 3.66 | 0 | Ionic (Protein Cationic) |
| I3 | CD1 | LEU- 17 | 3.47 | 0 | Hydrophobic |
| I5 | CG | LEU- 17 | 3.41 | 0 | Hydrophobic |
| C1 | CD1 | LEU- 17 | 3.75 | 0 | Hydrophobic |
| C5 | CD1 | LEU- 17 | 3.81 | 0 | Hydrophobic |
| C7 | CG2 | THR- 106 | 3.81 | 0 | Hydrophobic |
| C6' | CB | ALA- 108 | 4.46 | 0 | Hydrophobic |
| C1 | CB | ALA- 108 | 4.25 | 0 | Hydrophobic |
| C3' | CB | LEU- 110 | 4.34 | 0 | Hydrophobic |
| I3' | CB | LEU- 110 | 4.48 | 0 | Hydrophobic |
| I5 | CD1 | LEU- 110 | 3.3 | 0 | Hydrophobic |
| I5' | CD2 | LEU- 110 | 3.74 | 0 | Hydrophobic |
| C4' | CD2 | LEU- 110 | 3.87 | 0 | Hydrophobic |
| O4' | OG | SER- 117 | 3 | 166.17 | H-Bond (Protein Donor) |
| I3' | CB | SER- 117 | 4.16 | 0 | Hydrophobic |
| I5' | CB | SER- 117 | 3.65 | 0 | Hydrophobic |
| I3' | CG2 | THR- 119 | 3.25 | 0 | Hydrophobic |
| I5 | CG2 | THR- 119 | 3.38 | 0 | Hydrophobic |
| I5' | CB | THR- 119 | 3.71 | 0 | Hydrophobic |
| C5 | CG2 | THR- 119 | 3.78 | 0 | Hydrophobic |
| C2' | CG2 | THR- 119 | 3.72 | 0 | Hydrophobic |
| C6' | CG2 | THR- 119 | 3.44 | 0 | Hydrophobic |
