sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
3.300 Å
X-ray
2016-06-03
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.790 | 7.790 | 7.790 | 0.000 | 7.790 | 1 |
| Name: | Smoothened homolog |
|---|---|
| ID: | SMO_HUMAN |
| AC: | Q99835 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 0.000 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.743 | 540.000 |
| % Hydrophobic | % Polar |
|---|---|
| 60.00 | 40.00 |
| According to VolSite | |
| HET Code: | VIS |
|---|---|
| Formula: | C19H14Cl2N2O3S |
| Molecular weight: | 421.297 g/mol |
| DrugBank ID: | DB08828 |
| Buried Surface Area: | 66.64 % |
| Polar Surface area: | 84.51 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| -2.947 | 15.3956 | -73.8459 |
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 |
| C | CD1 | LEU- 221 | 3.66 | 0 | Hydrophobic |
| CL1 | SD | MET- 230 | 4.41 | 0 | Hydrophobic |
| C10 | CE | MET- 230 | 4.46 | 0 | Hydrophobic |
| CL1 | CH2 | TRP- 281 | 3.97 | 0 | Hydrophobic |
| C10 | CG1 | VAL- 386 | 4.02 | 0 | Hydrophobic |
| C9 | CB | VAL- 386 | 4.08 | 0 | Hydrophobic |
| C11 | CB | SER- 387 | 3.53 | 0 | Hydrophobic |
| N1 | OH | TYR- 394 | 2.87 | 140.51 | H-Bond (Protein Donor) |
| C13 | CE1 | TYR- 394 | 3.46 | 0 | Hydrophobic |
| CL | CB | ASP- 473 | 3.78 | 0 | Hydrophobic |
| C6 | CG | GLN- 477 | 4.31 | 0 | Hydrophobic |
| C | CB | TRP- 480 | 3.71 | 0 | Hydrophobic |
| C | CB | PHE- 484 | 4.1 | 0 | Hydrophobic |
| C | CG | PRO- 513 | 4.1 | 0 | Hydrophobic |
| C6 | CG | PRO- 513 | 3.8 | 0 | Hydrophobic |
| C11 | CB | GLU- 518 | 4.13 | 0 | Hydrophobic |
| C10 | CG | GLU- 518 | 4.22 | 0 | Hydrophobic |
| C16 | CB | ASN- 521 | 4.45 | 0 | Hydrophobic |
| CL1 | CD1 | LEU- 522 | 3.59 | 0 | Hydrophobic |
| C17 | CE | MET- 525 | 3.76 | 0 | Hydrophobic |
