sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.200 Å
X-ray
2007-12-14
| Name: | Polyamine oxidase FMS1 |
|---|---|
| ID: | FMS1_YEAST |
| AC: | P50264 |
| Organism: | Saccharomyces cerevisiae |
| Reign: | Eukaryota |
| TaxID: | 559292 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 31.480 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 3 |
| Cofactors: | FAD |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.063 | 1191.375 |
| % Hydrophobic | % Polar |
|---|---|
| 39.94 | 60.06 |
| According to VolSite | |
| HET Code: | SPJ |
|---|---|
| Formula: | C12H34N4 |
| Molecular weight: | 234.425 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 67.83 % |
| Polar Surface area: | 88.5 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 0 |
| H-Bond Donors: | 4 |
| Rings: | 0 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 4 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 11 |
| X | Y | Z |
|---|---|---|
| 97.0064 | 32.1587 | 53.3623 |
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 |
| C1M | CE3 | TRP- 65 | 3.84 | 0 | Hydrophobic |
| C1P | CZ2 | TRP- 65 | 4.13 | 0 | Hydrophobic |
| N1K | O | LEU- 173 | 3.34 | 121.9 | H-Bond (Ligand Donor) |
| C1A | CZ3 | TRP- 174 | 4.01 | 0 | Hydrophobic |
| C1D | CE3 | TRP- 174 | 4.3 | 0 | Hydrophobic |
| C1H | CE3 | TRP- 174 | 4.38 | 0 | Hydrophobic |
| C1I | CD2 | TRP- 174 | 3.74 | 0 | Hydrophobic |
| C1M | CZ2 | TRP- 174 | 3.94 | 0 | Hydrophobic |
| C1H | CD2 | LEU- 294 | 4.32 | 0 | Hydrophobic |
| C1P | CZ | PHE- 359 | 3.75 | 0 | Hydrophobic |
| C1D | CE1 | TYR- 450 | 3.63 | 0 | Hydrophobic |
| C1A | SG | CYS- 488 | 3.27 | 0 | Hydrophobic |
| C1D | SG | CYS- 488 | 4.36 | 0 | Hydrophobic |
| N1O | O | HOH- 827 | 3.35 | 168.99 | H-Bond (Ligand Donor) |
