sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.980 Å
X-ray
2014-04-05
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.090 | 8.110 | 7.800 | 0.980 | 9.440 | 3 |
| 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: | 40.060 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 22 |
| Non Standard Amino Acids: | 3 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | MG MG MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.773 | 1083.375 |
| % Hydrophobic | % Polar |
|---|---|
| 43.93 | 56.07 |
| According to VolSite | |
| HET Code: | RIS |
|---|---|
| Formula: | C7H7NO7P2 |
| Molecular weight: | 279.080 g/mol |
| DrugBank ID: | DB00884 |
| Buried Surface Area: | 69.43 % |
| Polar Surface area: | 179.12 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 |
|---|---|---|
| -15.9222 | 33.3421 | -8.30971 |
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 | PHE- 99 | 4.15 | 0 | Hydrophobic |
| C7 | CD2 | LEU- 100 | 3.61 | 0 | Hydrophobic |
| C1 | CB | ASP- 103 | 3.69 | 0 | Hydrophobic |
| O12 | CZ | ARG- 112 | 3.91 | 0 | Ionic (Protein Cationic) |
| O10 | CZ | ARG- 112 | 3.24 | 0 | Ionic (Protein Cationic) |
| O12 | NH2 | ARG- 112 | 2.9 | 147.11 | H-Bond (Protein Donor) |
| O10 | NH2 | ARG- 112 | 2.89 | 139.59 | H-Bond (Protein Donor) |
| O10 | NH1 | ARG- 112 | 2.75 | 146.98 | H-Bond (Protein Donor) |
| C6 | CG | GLN- 171 | 4.42 | 0 | Hydrophobic |
| O17 | NZ | LYS- 200 | 2.63 | 171.45 | H-Bond (Protein Donor) |
| O17 | NZ | LYS- 200 | 2.63 | 0 | Ionic (Protein Cationic) |
| O11 | NZ | LYS- 257 | 3.13 | 0 | Ionic (Protein Cationic) |
| O10 | NZ | LYS- 257 | 3 | 0 | Ionic (Protein Cationic) |
| O10 | NZ | LYS- 257 | 3 | 162.99 | H-Bond (Protein Donor) |
| O12 | MG | MG- 902 | 2.24 | 0 | Metal Acceptor |
| O15 | MG | MG- 902 | 2.08 | 0 | Metal Acceptor |
| O11 | MG | MG- 903 | 1.91 | 0 | Metal Acceptor |
| O16 | MG | MG- 903 | 1.97 | 0 | Metal Acceptor |
| O15 | MG | MG- 904 | 2.07 | 0 | Metal Acceptor |
