sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.310 Å
X-ray
2001-05-16
| Name: | Vitamin D-binding protein |
|---|---|
| ID: | VTDB_HUMAN |
| AC: | P02774 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 72.048 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.987 | 297.000 |
| % Hydrophobic | % Polar |
|---|---|
| 51.14 | 48.86 |
| According to VolSite | |
| HET Code: | VDY |
|---|---|
| Formula: | C27H44O2 |
| Molecular weight: | 400.637 g/mol |
| DrugBank ID: | DB00146 |
| Buried Surface Area: | 40.51 % |
| Polar Surface area: | 40.46 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -20.8527 | -56.9717 | 46.7958 |
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 |
| C26 | CG1 | VAL- 12 | 3.53 | 0 | Hydrophobic |
| C26 | CZ | PHE- 24 | 3.77 | 0 | Hydrophobic |
| C27 | CZ | PHE- 24 | 4.23 | 0 | Hydrophobic |
| C23 | CD1 | LEU- 31 | 3.76 | 0 | Hydrophobic |
| C27 | CD1 | LEU- 31 | 3.62 | 0 | Hydrophobic |
| O2 | OH | TYR- 32 | 2.85 | 120.96 | H-Bond (Protein Donor) |
| C14 | CZ | TYR- 32 | 4.31 | 0 | Hydrophobic |
| C15 | CE2 | TYR- 32 | 4.28 | 0 | Hydrophobic |
| C15 | CD | LYS- 35 | 4.2 | 0 | Hydrophobic |
| C1 | CZ | PHE- 36 | 4.21 | 0 | Hydrophobic |
| C26 | CG1 | VAL- 51 | 4.29 | 0 | Hydrophobic |
| O1 | OG | SER- 76 | 2.81 | 167.8 | H-Bond (Ligand Donor) |
| C4 | CB | SER- 76 | 4.03 | 0 | Hydrophobic |
| C3 | CB | MET- 107 | 3.63 | 0 | Hydrophobic |
