sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
2012-04-14
| 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: | 30.432 |
|---|---|
| Number of residues: | 40 |
| Including | |
| Standard Amino Acids: | 39 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.948 | 536.625 |
| % Hydrophobic | % Polar |
|---|---|
| 73.58 | 26.42 |
| According to VolSite | |
| HET Code: | YS3 |
|---|---|
| Formula: | C26H42O3 |
| Molecular weight: | 402.610 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 66.94 % |
| Polar Surface area: | 60.69 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| -15.3201 | 25.0519 | -3.28507 |
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 |
| CAX | CE2 | TYR- 143 | 4.47 | 0 | Hydrophobic |
| CAY | CZ | TYR- 143 | 4.31 | 0 | Hydrophobic |
| OAG | OH | TYR- 143 | 2.76 | 147.79 | H-Bond (Protein Donor) |
| CAY | CE2 | TYR- 147 | 3.75 | 0 | Hydrophobic |
| CAY | CZ | PHE- 150 | 4.23 | 0 | Hydrophobic |
| CAC | CD1 | LEU- 223 | 3.6 | 0 | Hydrophobic |
| CAE | CD2 | LEU- 226 | 4.27 | 0 | Hydrophobic |
| CAK | CD2 | LEU- 226 | 4.24 | 0 | Hydrophobic |
| CAE | CD2 | LEU- 229 | 4.41 | 0 | Hydrophobic |
| CAR | CD1 | LEU- 229 | 4.01 | 0 | Hydrophobic |
| CAI | CD2 | LEU- 229 | 3.77 | 0 | Hydrophobic |
| CAD | CG2 | VAL- 230 | 3.69 | 0 | Hydrophobic |
| CAE | CG2 | VAL- 230 | 3.59 | 0 | Hydrophobic |
| CAM | CG2 | VAL- 230 | 3.82 | 0 | Hydrophobic |
| CAX | CB | SER- 233 | 4.47 | 0 | Hydrophobic |
| OAF | OG | SER- 233 | 2.71 | 165.37 | H-Bond (Ligand Donor) |
| CAN | CD1 | ILE- 264 | 4.02 | 0 | Hydrophobic |
| CAQ | CG2 | ILE- 267 | 4.01 | 0 | Hydrophobic |
| CAR | CG2 | ILE- 267 | 4.08 | 0 | Hydrophobic |
| CAQ | CG | MET- 268 | 4.42 | 0 | Hydrophobic |
| CAX | CG | ARG- 270 | 4.06 | 0 | Hydrophobic |
| OAF | NH1 | ARG- 270 | 2.69 | 142.52 | H-Bond (Protein Donor) |
| CAU | CB | SER- 271 | 3.68 | 0 | Hydrophobic |
| CAY | CB | SER- 274 | 4.24 | 0 | Hydrophobic |
| OAG | OG | SER- 274 | 3.13 | 166.01 | H-Bond (Ligand Donor) |
| CAK | CE3 | TRP- 282 | 4.18 | 0 | Hydrophobic |
| CAL | CD2 | TRP- 282 | 3.29 | 0 | Hydrophobic |
| CAS | SG | CYS- 284 | 3.41 | 0 | Hydrophobic |
| CAK | CB | TYR- 291 | 4.12 | 0 | Hydrophobic |
| CAB | CG1 | VAL- 296 | 3.82 | 0 | Hydrophobic |
| CAO | CG2 | VAL- 296 | 3.43 | 0 | Hydrophobic |
| OAH | NE2 | HIS- 301 | 2.76 | 148.89 | H-Bond (Ligand Donor) |
| CAB | CD2 | LEU- 305 | 3.84 | 0 | Hydrophobic |
| OAH | NE2 | HIS- 393 | 2.77 | 155.44 | H-Bond (Protein Donor) |
| CAD | CE1 | PHE- 418 | 3.92 | 0 | Hydrophobic |
