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
2010-12-13
| Name: | Homoisocitrate dehydrogenase |
|---|---|
| ID: | HICDH_THET8 |
| AC: | Q5SIJ1 |
| Organism: | Thermus thermophilus |
| Reign: | Bacteria |
| TaxID: | 300852 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 78 % |
| B | 22 % |
| B-Factor: | 28.580 |
|---|---|
| Number of residues: | 23 |
| Including | |
| Standard Amino Acids: | 23 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.366 | 864.000 |
| % Hydrophobic | % Polar |
|---|---|
| 34.77 | 65.23 |
| According to VolSite | |
| HET Code: | XYN |
|---|---|
| Formula: | C5H4O5S |
| Molecular weight: | 176.147 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 59.68 % |
| Polar Surface area: | 122.63 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 0 |
| Rings: | 0 |
| Aromatic rings: | 0 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 33.2684 | -52.0695 | -36.1274 |
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 |
| OBD | NH1 | ARG- 118 | 2.72 | 172.41 | H-Bond (Protein Donor) |
| OBD | NH2 | ARG- 118 | 3.41 | 129.99 | H-Bond (Protein Donor) |
| OBD | CZ | ARG- 118 | 3.5 | 0 | Ionic (Protein Cationic) |
| OBA | OH | TYR- 125 | 2.59 | 173.27 | H-Bond (Protein Donor) |
| OBB | OD2 | ASP- 232 | 2.9 | 161.59 | H-Bond (Ligand Donor) |
| CBG | CG1 | VAL- 259 | 4.22 | 0 | Hydrophobic |
