sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
3.200 Å
X-ray
2016-06-03
| 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 |
|---|---|
| A | 100 % |
| B-Factor: | 0.000 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.029 | 587.250 |
| % Hydrophobic | % Polar |
|---|---|
| 60.92 | 39.08 |
| According to VolSite | |
| HET Code: | CLR |
|---|---|
| Formula: | C27H46O |
| Molecular weight: | 386.654 g/mol |
| DrugBank ID: | DB04540 |
| Buried Surface Area: | 61.07 % |
| Polar Surface area: | 20.23 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 1 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| -34.4683 | -2.25039 | 98.9877 |
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 |
| O1 | OD2 | ASP- 95 | 2.78 | 166.32 | H-Bond (Ligand Donor) |
| C2 | CD | LYS- 105 | 3.75 | 0 | Hydrophobic |
| C1 | CB | LEU- 108 | 3.93 | 0 | Hydrophobic |
| C2 | CD1 | LEU- 108 | 4.17 | 0 | Hydrophobic |
| C11 | CB | LEU- 108 | 4.2 | 0 | Hydrophobic |
| C4 | CZ2 | TRP- 109 | 4.44 | 0 | Hydrophobic |
| C11 | CD2 | TRP- 109 | 4.3 | 0 | Hydrophobic |
| C14 | CZ3 | TRP- 109 | 4.34 | 0 | Hydrophobic |
| C1 | CE2 | TRP- 109 | 3.68 | 0 | Hydrophobic |
| C7 | CH2 | TRP- 109 | 3.64 | 0 | Hydrophobic |
| C1 | CE2 | TRP- 109 | 3.68 | 0 | Hydrophobic |
| C21 | CD1 | LEU- 112 | 4.03 | 0 | Hydrophobic |
| C22 | CG | LEU- 112 | 4.11 | 0 | Hydrophobic |
| C17 | CD1 | LEU- 112 | 3.68 | 0 | Hydrophobic |
| C27 | CB | ASN- 114 | 4.08 | 0 | Hydrophobic |
| C27 | CB | ALA- 115 | 4.11 | 0 | Hydrophobic |
| C22 | CD1 | ILE- 156 | 4.4 | 0 | Hydrophobic |
| C24 | CD1 | ILE- 156 | 3.78 | 0 | Hydrophobic |
| C7 | CG1 | VAL- 157 | 4.1 | 0 | Hydrophobic |
| C15 | CG1 | VAL- 157 | 4.23 | 0 | Hydrophobic |
| C7 | CB | ARG- 161 | 3.91 | 0 | Hydrophobic |
| C8 | CD | ARG- 161 | 4.17 | 0 | Hydrophobic |
| C15 | CB | ARG- 161 | 4.07 | 0 | Hydrophobic |
| C19 | CD | ARG- 161 | 4.01 | 0 | Hydrophobic |
| C4 | CG | PRO- 164 | 4.3 | 0 | Hydrophobic |
| C26 | CG2 | VAL- 210 | 3.58 | 0 | Hydrophobic |
| C26 | CD2 | LEU- 489 | 3.98 | 0 | Hydrophobic |
| C25 | CB | ALA- 492 | 3.55 | 0 | Hydrophobic |
| C12 | CD1 | ILE- 496 | 4.24 | 0 | Hydrophobic |
| C18 | CD1 | ILE- 496 | 3.97 | 0 | Hydrophobic |
| C21 | CD1 | ILE- 496 | 4.31 | 0 | Hydrophobic |
