sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.100 Å
X-ray
2011-05-11
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.750 | 7.580 | 7.580 | 0.830 | 8.410 | 2 |
| Name: | Farnesyl pyrophosphate synthase |
|---|---|
| ID: | FPPS_HUMAN |
| AC: | P14324 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.5.1.10 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 34.373 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 3 |
| Water Molecules: | 4 |
| Cofactors: | |
| Metals: | MG MG MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.712 | 921.375 |
| % Hydrophobic | % Polar |
|---|---|
| 42.49 | 57.51 |
| According to VolSite | |
| HET Code: | UNR |
|---|---|
| Formula: | C8H10NO7P2 |
| Molecular weight: | 294.115 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 72.51 % |
| Polar Surface area: | 170.11 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 1 |
| Rings: | 1 |
| Aromatic rings: | 1 |
| Anionic atoms: | 4 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 15.6224 | -33.0593 | 26.0275 |
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 |
| C3 | CD2 | LEU- 100 | 3.97 | 0 | Hydrophobic |
| O9 | CZ | ARG- 112 | 3.84 | 0 | Ionic (Protein Cationic) |
| O10 | CZ | ARG- 112 | 3.14 | 0 | Ionic (Protein Cationic) |
| O9 | NH2 | ARG- 112 | 2.81 | 139.11 | H-Bond (Protein Donor) |
| O10 | NH1 | ARG- 112 | 2.54 | 152.52 | H-Bond (Protein Donor) |
| O10 | NH2 | ARG- 112 | 2.89 | 133.3 | H-Bond (Protein Donor) |
| O7 | NZ | LYS- 200 | 2.58 | 154.79 | H-Bond (Protein Donor) |
| O7 | NZ | LYS- 200 | 2.58 | 0 | Ionic (Protein Cationic) |
| C25 | CG | LYS- 200 | 3.92 | 0 | Hydrophobic |
| C25 | CB | THR- 201 | 4.25 | 0 | Hydrophobic |
| O2 | OD2 | ASP- 243 | 2.88 | 166.27 | H-Bond (Ligand Donor) |
| O8 | NZ | LYS- 257 | 3.43 | 0 | Ionic (Protein Cationic) |
| O10 | NZ | LYS- 257 | 3.24 | 0 | Ionic (Protein Cationic) |
| O10 | NZ | LYS- 257 | 3.24 | 154.02 | H-Bond (Protein Donor) |
| O5 | MG | MG- 907 | 2.07 | 0 | Metal Acceptor |
| O9 | MG | MG- 907 | 2.03 | 0 | Metal Acceptor |
| O6 | MG | MG- 908 | 2.01 | 0 | Metal Acceptor |
| O8 | MG | MG- 908 | 1.97 | 0 | Metal Acceptor |
| O5 | MG | MG- 909 | 2.19 | 0 | Metal Acceptor |
