sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
2005-06-03
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.070 | 8.610 | 8.610 | 1.540 | 10.150 | 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: | 43.680 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 24 |
| Non Standard Amino Acids: | 4 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | MG MG MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.163 | 634.500 |
| % Hydrophobic | % Polar |
|---|---|
| 46.28 | 53.72 |
| According to VolSite | |
| HET Code: | ZOL |
|---|---|
| Formula: | C5H6N2O7P2 |
| Molecular weight: | 268.058 g/mol |
| DrugBank ID: | DB00399 |
| Buried Surface Area: | 68.03 % |
| 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 |
|---|---|---|
| 15.1554 | 33.5146 | -8.38031 |
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- 114 | 4.12 | 0 | Hydrophobic |
| O10 | NH1 | ARG- 126 | 2.84 | 142.52 | H-Bond (Protein Donor) |
| O10 | NH2 | ARG- 126 | 2.79 | 145.12 | H-Bond (Protein Donor) |
| O11 | NH2 | ARG- 126 | 3.31 | 134.76 | H-Bond (Protein Donor) |
| O10 | CZ | ARG- 126 | 3.24 | 0 | Ionic (Protein Cationic) |
| O15 | NZ | LYS- 214 | 2.91 | 140.02 | H-Bond (Protein Donor) |
| O15 | NZ | LYS- 214 | 2.91 | 0 | Ionic (Protein Cationic) |
| O13 | OD2 | ASP- 257 | 2.78 | 162.9 | H-Bond (Ligand Donor) |
| O10 | NZ | LYS- 271 | 2.99 | 168.83 | H-Bond (Protein Donor) |
| O12 | NZ | LYS- 271 | 2.94 | 123.1 | H-Bond (Protein Donor) |
| O10 | NZ | LYS- 271 | 2.99 | 0 | Ionic (Protein Cationic) |
| O12 | NZ | LYS- 271 | 2.94 | 0 | Ionic (Protein Cationic) |
| O17 | MG | MG- 907 | 2.17 | 0 | Metal Acceptor |
| O11 | MG | MG- 907 | 2.18 | 0 | Metal Acceptor |
| O16 | MG | MG- 908 | 2.18 | 0 | Metal Acceptor |
| O12 | MG | MG- 908 | 2.15 | 0 | Metal Acceptor |
| O17 | MG | MG- 909 | 2.17 | 0 | Metal Acceptor |
