sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.140 Å
X-ray
2007-01-24
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.590 | 6.590 | 6.590 | 0.000 | 6.590 | 1 |
| 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 |
|---|---|
| B | 100 % |
| B-Factor: | 36.645 |
|---|---|
| Number of residues: | 24 |
| Including | |
| Standard Amino Acids: | 20 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | MG MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.437 | 955.125 |
| % Hydrophobic | % Polar |
|---|---|
| 36.04 | 63.96 |
| According to VolSite | |
| HET Code: | ZOL |
|---|---|
| Formula: | C5H6N2O7P2 |
| Molecular weight: | 268.058 g/mol |
| DrugBank ID: | DB00399 |
| Buried Surface Area: | 62.38 % |
| Polar Surface area: | 184.05 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: | 4 |
| X | Y | Z |
|---|---|---|
| 24.7478 | 25.7204 | 29.7328 |
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 |
| C7 | CD2 | LEU- 77 | 4.12 | 0 | Hydrophobic |
| O17 | NH2 | ARG- 89 | 3.32 | 130.34 | H-Bond (Protein Donor) |
| O15 | NH1 | ARG- 89 | 2.92 | 150.29 | H-Bond (Protein Donor) |
| O15 | NH2 | ARG- 89 | 3.41 | 131.2 | H-Bond (Protein Donor) |
| O15 | CZ | ARG- 89 | 3.61 | 0 | Ionic (Protein Cationic) |
| O11 | NZ | LYS- 174 | 2.87 | 139.25 | H-Bond (Protein Donor) |
| O11 | NZ | LYS- 174 | 2.87 | 0 | Ionic (Protein Cationic) |
| N17 | OG1 | THR- 175 | 3.27 | 153.99 | H-Bond (Protein Donor) |
| O16 | OD2 | ASP- 214 | 3.03 | 155.15 | H-Bond (Protein Donor) |
| O12 | OD2 | ASP- 214 | 3.29 | 123.79 | H-Bond (Protein Donor) |
| O10 | NZ | LYS- 238 | 3.87 | 0 | Ionic (Protein Cationic) |
| O12 | NZ | LYS- 238 | 2.71 | 0 | Ionic (Protein Cationic) |
| O12 | NZ | LYS- 238 | 2.71 | 143.77 | H-Bond (Protein Donor) |
| O17 | MG | MG- 1303 | 1.91 | 0 | Metal Acceptor |
| O10 | MG | MG- 1303 | 2.07 | 0 | Metal Acceptor |
| O10 | MG | MG- 1304 | 2.14 | 0 | Metal Acceptor |
