sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.280 Å
X-ray
2006-08-13
| Name: | Farnesyl pyrophosphate synthase |
|---|---|
| ID: | Q86C09_9TRYP |
| AC: | Q86C09 |
| Organism: | Trypanosoma brucei |
| Reign: | Eukaryota |
| TaxID: | 5691 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 28.526 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 3 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | MG MG MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.673 | 1292.625 |
| % Hydrophobic | % Polar |
|---|---|
| 32.64 | 67.36 |
| According to VolSite | |
| HET Code: | 1BY |
|---|---|
| Formula: | C7H8N2O6P2 |
| Molecular weight: | 278.096 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 61.4 % |
| Polar Surface area: | 170.92 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 1 |
| Rings: | 1 |
| Aromatic rings: | 1 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 19.5001 | 16.4215 | 41.4691 |
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 |
| C6 | CB | TYR- 99 | 3.59 | 0 | Hydrophobic |
| C4 | CD1 | LEU- 100 | 4.1 | 0 | Hydrophobic |
| C2 | CD1 | LEU- 100 | 3.88 | 0 | Hydrophobic |
| C4 | CB | ASP- 103 | 3.77 | 0 | Hydrophobic |
| O1 | CZ | ARG- 112 | 3.78 | 0 | Ionic (Protein Cationic) |
| O2 | NH2 | ARG- 112 | 3.05 | 133.14 | H-Bond (Protein Donor) |
| C6 | CG2 | THR- 168 | 3.9 | 0 | Hydrophobic |
| C6 | CG | GLN- 172 | 3.64 | 0 | Hydrophobic |
| O5 | NZ | LYS- 212 | 2.62 | 156.61 | H-Bond (Protein Donor) |
| O5 | NZ | LYS- 212 | 2.62 | 0 | Ionic (Protein Cationic) |
| O2 | MG | MG- 4002 | 1.97 | 0 | Metal Acceptor |
| O4 | MG | MG- 4002 | 2.26 | 0 | Metal Acceptor |
| O4 | MG | MG- 4004 | 2.16 | 0 | Metal Acceptor |
