sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.600 Å
X-ray
2014-05-31
| 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: | 39 |
| Including | |
| Standard Amino Acids: | 39 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.301 | 1130.625 |
| % Hydrophobic | % Polar |
|---|---|
| 57.91 | 42.09 |
| According to VolSite | |
| HET Code: | SG8 |
|---|---|
| Formula: | C28H27ClF2N3OS |
| Molecular weight: | 527.048 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 73.74 % |
| Polar Surface area: | 78.05 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 1 |
| Rings: | 5 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -21.531 | 62.9477 | -1.50786 |
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 |
| F1 | CG1 | ILE- 215 | 3.92 | 0 | Hydrophobic |
| O1 | ND2 | ASN- 219 | 3.19 | 159.33 | H-Bond (Protein Donor) |
| F1 | CG | PRO- 220 | 4.22 | 0 | Hydrophobic |
| CL1 | CD2 | LEU- 221 | 4.47 | 0 | Hydrophobic |
| S1 | CD1 | LEU- 221 | 4.11 | 0 | Hydrophobic |
| C4 | CD1 | LEU- 221 | 3.59 | 0 | Hydrophobic |
| C5 | CD1 | LEU- 221 | 3.54 | 0 | Hydrophobic |
| F1 | CE | MET- 301 | 3.3 | 0 | Hydrophobic |
| C15 | CE | MET- 301 | 3.82 | 0 | Hydrophobic |
| C27 | CE | MET- 301 | 3.5 | 0 | Hydrophobic |
| C27 | CD1 | LEU- 303 | 3.73 | 0 | Hydrophobic |
| C15 | CD2 | LEU- 303 | 3.74 | 0 | Hydrophobic |
| C22 | CB | ASP- 384 | 4.21 | 0 | Hydrophobic |
| C13 | CB | ASP- 384 | 3.9 | 0 | Hydrophobic |
| C21 | CE1 | TYR- 394 | 3.48 | 0 | Hydrophobic |
| C13 | CB | TYR- 394 | 3.54 | 0 | Hydrophobic |
| C24 | CG | LYS- 395 | 4.16 | 0 | Hydrophobic |
| C27 | CG | LYS- 395 | 3.76 | 0 | Hydrophobic |
| C28 | CB | LYS- 395 | 3.75 | 0 | Hydrophobic |
| C19 | CB | ASP- 473 | 3.83 | 0 | Hydrophobic |
| N2 | OD2 | ASP- 473 | 3.08 | 144.21 | H-Bond (Ligand Donor) |
| N2 | OD2 | ASP- 473 | 3.08 | 0 | Ionic (Ligand Cationic) |
| CL1 | CG | GLN- 477 | 3.97 | 0 | Hydrophobic |
| CL1 | CE3 | TRP- 480 | 3.64 | 0 | Hydrophobic |
| C18 | CZ3 | TRP- 480 | 4.18 | 0 | Hydrophobic |
| F2 | CB | TRP- 480 | 3.97 | 0 | Hydrophobic |
| C24 | CG | GLU- 481 | 4.02 | 0 | Hydrophobic |
| F2 | CG | GLU- 481 | 3.32 | 0 | Hydrophobic |
| F1 | CE2 | PHE- 484 | 4.27 | 0 | Hydrophobic |
| C1 | CB | PHE- 484 | 4.25 | 0 | Hydrophobic |
| C2 | CG | PHE- 484 | 3.36 | 0 | Hydrophobic |
| CL1 | CG | PRO- 513 | 3.9 | 0 | Hydrophobic |
| C18 | CG | PRO- 513 | 4.2 | 0 | Hydrophobic |
