sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.010 Å
X-ray
2007-06-26
| Name: | Geranylgeranyl pyrophosphate synthase |
|---|---|
| ID: | GGPPS_YEAST |
| AC: | Q12051 |
| Organism: | Saccharomyces cerevisiae |
| Reign: | Eukaryota |
| TaxID: | 559292 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 96 % |
| B | 4 % |
| B-Factor: | 29.994 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 24 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.861 | 1080.000 |
| % Hydrophobic | % Polar |
|---|---|
| 40.00 | 60.00 |
| According to VolSite | |
| HET Code: | 028 |
|---|---|
| Formula: | C7H14O7P2 |
| Molecular weight: | 272.129 g/mol |
| DrugBank ID: | DB06830 |
| Buried Surface Area: | 48.73 % |
| Polar Surface area: | 166.23 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 1 |
| Rings: | 0 |
| Aromatic rings: | 0 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 28.3798 | 46.8633 | 7.48837 |
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 |
| CAJ | CB | SER- 76 | 4.32 | 0 | Hydrophobic |
| CAK | CD2 | LEU- 77 | 4.17 | 0 | Hydrophobic |
| CAM | CD2 | LEU- 77 | 4.45 | 0 | Hydrophobic |
| CAI | CB | ASP- 80 | 3.87 | 0 | Hydrophobic |
| OAD | OD2 | ASP- 80 | 2.84 | 151.24 | H-Bond (Ligand Donor) |
| OAG | NH2 | ARG- 89 | 2.87 | 158.32 | H-Bond (Protein Donor) |
| OAG | NH1 | ARG- 89 | 3.19 | 139.2 | H-Bond (Protein Donor) |
| OAG | CZ | ARG- 89 | 3.48 | 0 | Ionic (Protein Cationic) |
| CAA | CD1 | LEU- 143 | 3.9 | 0 | Hydrophobic |
| CAJ | CD1 | LEU- 143 | 4.1 | 0 | Hydrophobic |
| CAA | CG | GLN- 147 | 3.83 | 0 | Hydrophobic |
| OAF | NZ | LYS- 174 | 3.58 | 0 | Ionic (Protein Cationic) |
| OAB | NZ | LYS- 174 | 3.43 | 0 | Ionic (Protein Cationic) |
| OAB | NZ | LYS- 174 | 3.43 | 148.46 | H-Bond (Protein Donor) |
| OAB | NE2 | GLN- 211 | 2.94 | 137.32 | H-Bond (Protein Donor) |
| OAE | NZ | LYS- 238 | 3.04 | 0 | Ionic (Protein Cationic) |
| OAF | NZ | LYS- 238 | 2.71 | 0 | Ionic (Protein Cationic) |
| OAF | NZ | LYS- 238 | 2.71 | 167.13 | H-Bond (Protein Donor) |
