sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.550 Å
X-ray
2014-11-27
| Name: | Thyroxine-binding globulin |
|---|---|
| ID: | THBG_HUMAN |
| AC: | P05543 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 15.854 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.681 | 381.375 |
| % Hydrophobic | % Polar |
|---|---|
| 48.67 | 51.33 |
| According to VolSite | |
| HET Code: | T44 |
|---|---|
| Formula: | C15H10I4NO4 |
| Molecular weight: | 775.862 g/mol |
| DrugBank ID: | DB00451 |
| Buried Surface Area: | 62.44 % |
| 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 |
|---|---|---|
| -9.02325 | 7.40129 | -20.7754 |
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 |
| I5' | CB | SER- 23 | 4.21 | 0 | Hydrophobic |
| I5' | CB | ALA- 27 | 3.86 | 0 | Hydrophobic |
| I3 | CD2 | LEU- 246 | 4.5 | 0 | Hydrophobic |
| C2 | CD2 | LEU- 246 | 3.89 | 0 | Hydrophobic |
| C1 | CD1 | LEU- 246 | 3.87 | 0 | Hydrophobic |
| I5 | CD1 | LEU- 248 | 4.14 | 0 | Hydrophobic |
| C1' | CB | LEU- 269 | 4.18 | 0 | Hydrophobic |
| C5' | CB | LEU- 269 | 4.18 | 0 | Hydrophobic |
| C6' | CD1 | LEU- 269 | 3.73 | 0 | Hydrophobic |
| I5 | CB | LEU- 269 | 4.45 | 0 | Hydrophobic |
| I5' | CD1 | LEU- 269 | 4.33 | 0 | Hydrophobic |
| O4' | NZ | LYS- 270 | 2.73 | 162.7 | H-Bond (Protein Donor) |
| I3' | CG | LYS- 270 | 3.93 | 0 | Hydrophobic |
| C4' | CG | LYS- 270 | 4.24 | 0 | Hydrophobic |
| I5 | CB | TRP- 272 | 4.27 | 0 | Hydrophobic |
| C5 | CB | ASN- 273 | 4.41 | 0 | Hydrophobic |
| I3' | CB | ASN- 273 | 3.9 | 0 | Hydrophobic |
| I5 | CB | ASN- 273 | 4.07 | 0 | Hydrophobic |
| C2' | CB | ASN- 273 | 4.07 | 0 | Hydrophobic |
| N8 | OD1 | ASN- 273 | 2.78 | 136.69 | H-Bond (Ligand Donor) |
| C6 | CD1 | LEU- 276 | 4.47 | 0 | Hydrophobic |
| I5 | CD1 | LEU- 276 | 4.48 | 0 | Hydrophobic |
| I3 | CB | LEU- 376 | 4.02 | 0 | Hydrophobic |
| C4 | CD1 | LEU- 376 | 3.52 | 0 | Hydrophobic |
| O10 | CZ | ARG- 378 | 3.47 | 0 | Ionic (Protein Cationic) |
| O10 | NH1 | ARG- 378 | 2.63 | 128.32 | H-Bond (Protein Donor) |
| I3 | CG | ARG- 381 | 3.98 | 0 | Hydrophobic |
| I5' | CB | ARG- 381 | 4.49 | 0 | Hydrophobic |
| C4' | CD | ARG- 381 | 3.88 | 0 | Hydrophobic |
| O9 | O | HOH- 594 | 3.02 | 137.16 | H-Bond (Protein Donor) |
| O4' | O | HOH- 635 | 2.58 | 141.69 | H-Bond (Protein Donor) |
