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
2013-02-05
| Name: | Vitamin D3 receptor |
|---|---|
| ID: | VDR_RAT |
| AC: | P13053 |
| Organism: | Rattus norvegicus |
| Reign: | Eukaryota |
| TaxID: | 10116 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 37.685 |
|---|---|
| Number of residues: | 42 |
| Including | |
| Standard Amino Acids: | 39 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.849 | 553.500 |
| % Hydrophobic | % Polar |
|---|---|
| 72.56 | 27.44 |
| According to VolSite | |
| HET Code: | 3KL |
|---|---|
| Formula: | C24H37O3 |
| Molecular weight: | 373.549 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 69.48 % |
| Polar Surface area: | 57.2 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 0 |
| Rings: | 4 |
| Aromatic rings: | 0 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 12.9829 | 3.962 | 25.0629 |
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 | CB | LEU- 226 | 3.95 | 0 | Hydrophobic |
| C1 | CD1 | LEU- 226 | 4.35 | 0 | Hydrophobic |
| C11 | CD1 | LEU- 226 | 3.97 | 0 | Hydrophobic |
| C12 | CD2 | LEU- 226 | 4.17 | 0 | Hydrophobic |
| C12 | CD1 | LEU- 229 | 4.44 | 0 | Hydrophobic |
| C17 | CD1 | LEU- 229 | 4.1 | 0 | Hydrophobic |
| C21 | CD1 | LEU- 229 | 4.1 | 0 | Hydrophobic |
| C2 | CG2 | VAL- 230 | 3.85 | 0 | Hydrophobic |
| C4 | CG2 | VAL- 230 | 3.82 | 0 | Hydrophobic |
| C9 | CG2 | VAL- 230 | 4.26 | 0 | Hydrophobic |
| C4 | CD1 | ILE- 264 | 4.5 | 0 | Hydrophobic |
| C7 | CD1 | ILE- 264 | 3.77 | 0 | Hydrophobic |
| C16 | CG2 | ILE- 267 | 3.67 | 0 | Hydrophobic |
| C15 | CG | MET- 268 | 4.3 | 0 | Hydrophobic |
| C6 | CE | MET- 268 | 4.02 | 0 | Hydrophobic |
| C23 | CB | SER- 271 | 3.56 | 0 | Hydrophobic |
| C16 | CB | SER- 271 | 3.59 | 0 | Hydrophobic |
| C22 | CB | SER- 271 | 3.3 | 0 | Hydrophobic |
| C23 | CB | SER- 274 | 4.25 | 0 | Hydrophobic |
| OT1 | OG | SER- 274 | 2.81 | 151.04 | H-Bond (Protein Donor) |
| C18 | CH2 | TRP- 282 | 3.76 | 0 | Hydrophobic |
| C20 | CD2 | TRP- 282 | 4.27 | 0 | Hydrophobic |
| C21 | CB | TRP- 282 | 4.2 | 0 | Hydrophobic |
| C23 | CB | TRP- 282 | 4.41 | 0 | Hydrophobic |
| C23 | SG | CYS- 284 | 3.79 | 0 | Hydrophobic |
| C21 | CD1 | TYR- 291 | 3.72 | 0 | Hydrophobic |
| C11 | CG1 | VAL- 296 | 4.11 | 0 | Hydrophobic |
| C12 | CG2 | VAL- 296 | 4.47 | 0 | Hydrophobic |
| C18 | CG2 | VAL- 296 | 3.8 | 0 | Hydrophobic |
| C19 | CG1 | VAL- 296 | 3.64 | 0 | Hydrophobic |
| C1 | CB | ALA- 299 | 3.9 | 0 | Hydrophobic |
| C19 | CB | HIS- 301 | 4.25 | 0 | Hydrophobic |
| C6 | CD2 | LEU- 305 | 3.84 | 0 | Hydrophobic |
| C19 | CD1 | ILE- 306 | 3.77 | 0 | Hydrophobic |
| C15 | CD2 | LEU- 309 | 4.28 | 0 | Hydrophobic |
| C18 | CD2 | LEU- 309 | 4.45 | 0 | Hydrophobic |
| C8 | CD2 | LEU- 309 | 4.15 | 0 | Hydrophobic |
| OT2 | O | HOH- 701 | 2.75 | 179.98 | H-Bond (Protein Donor) |
