sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.420 Å
X-ray
2015-01-19
| Name: | Homospermidine synthase |
|---|---|
| ID: | HSS_BLAVI |
| AC: | O32323 |
| Organism: | Blastochloris viridis |
| Reign: | Bacteria |
| TaxID: | 1079 |
| EC Number: | 2.5.1.44 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 21 % |
| B | 79 % |
| B-Factor: | 18.035 |
|---|---|
| Number of residues: | 13 |
| Including | |
| Standard Amino Acids: | 13 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.920 | 1015.875 |
| % Hydrophobic | % Polar |
|---|---|
| 36.21 | 63.79 |
| According to VolSite | |
| HET Code: | 1PS |
|---|---|
| Formula: | C8H11NO3S |
| Molecular weight: | 201.243 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 44.84 % |
| Polar Surface area: | 69.45 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 0 |
| Rings: | 1 |
| Aromatic rings: | 1 |
| Anionic atoms: | 1 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 13.3521 | 15.2789 | 7.34362 |
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 |
| C2 | CD2 | LEU- 239 | 4.08 | 0 | Hydrophobic |
| C2 | CG | MET- 338 | 3.59 | 0 | Hydrophobic |
| C8 | CB | LYS- 343 | 4.41 | 0 | Hydrophobic |
| C8 | CG | ARG- 344 | 3.74 | 0 | Hydrophobic |
| O2 | N | ARG- 344 | 2.5 | 133.87 | H-Bond (Protein Donor) |
