sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
3.000 Å
X-ray
2004-06-29
| Name: | Homoserine dehydrogenase |
|---|---|
| ID: | DHOM_YEAST |
| AC: | P31116 |
| Organism: | Saccharomyces cerevisiae |
| Reign: | Eukaryota |
| TaxID: | 559292 |
| EC Number: | 1.1.1.3 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 33.365 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 29 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.202 | 563.625 |
| % Hydrophobic | % Polar |
|---|---|
| 36.53 | 63.47 |
| According to VolSite | |
| HET Code: | 178 |
|---|---|
| Formula: | C18H22O2S |
| Molecular weight: | 302.431 g/mol |
| DrugBank ID: | DB02881 |
| Buried Surface Area: | 44.42 % |
| Polar Surface area: | 65.76 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 38.8243 | 43.7317 | -20.128 |
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 |
| C2A | CB | SER- 94 | 3.76 | 0 | Hydrophobic |
| C2B | CD | LYS- 117 | 3.26 | 0 | Hydrophobic |
| C2G | CG | LYS- 117 | 3.29 | 0 | Hydrophobic |
| O' | OG | SER- 174 | 3.33 | 120.87 | H-Bond (Ligand Donor) |
| O' | N | GLY- 175 | 2.6 | 148.24 | H-Bond (Protein Donor) |
| C2Y | CG2 | THR- 176 | 3.87 | 0 | Hydrophobic |
| C2Z | CG | GLU- 208 | 4.29 | 0 | Hydrophobic |
