sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.800 Å
X-ray
2013-03-25
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 5.500 | 5.500 | 5.500 | 0.000 | 5.500 | 1 |
| 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 |
|---|---|
| F | 100 % |
| B-Factor: | 56.426 |
|---|---|
| Number of residues: | 40 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 3 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | MG MG MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.151 | 472.500 |
| % Hydrophobic | % Polar |
|---|---|
| 47.86 | 52.14 |
| According to VolSite | |
| HET Code: | 1MV |
|---|---|
| Formula: | C14H11N3O6P2S |
| Molecular weight: | 411.266 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 62.58 % |
| Polar Surface area: | 212.05 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 9 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 15.6113 | 30.992 | -7.98165 |
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 |
| CAQ | CD1 | PHE- 99 | 4.45 | 0 | Hydrophobic |
| CAP | CB | PHE- 99 | 3.42 | 0 | Hydrophobic |
| CAP | CB | ASP- 103 | 3.5 | 0 | Hydrophobic |
| CAO | CE | MET- 106 | 3.77 | 0 | Hydrophobic |
| OAX | NH1 | ARG- 112 | 2.98 | 124.85 | H-Bond (Protein Donor) |
| OAX | CZ | ARG- 112 | 3.08 | 0 | Ionic (Protein Cationic) |
| SAE | CG2 | THR- 167 | 3.53 | 0 | Hydrophobic |
| CAL | CG2 | THR- 167 | 3.28 | 0 | Hydrophobic |
| CAM | CB | GLN- 171 | 3.28 | 0 | Hydrophobic |
| CAN | CG | GLN- 171 | 3.7 | 0 | Hydrophobic |
| OAU | NZ | LYS- 200 | 2.72 | 147.23 | H-Bond (Protein Donor) |
| OAW | NZ | LYS- 200 | 3.36 | 126.01 | H-Bond (Protein Donor) |
| OAU | NZ | LYS- 200 | 2.72 | 0 | Ionic (Protein Cationic) |
| OAW | NZ | LYS- 200 | 3.36 | 0 | Ionic (Protein Cationic) |
| SAE | CB | LYS- 200 | 4.46 | 0 | Hydrophobic |
| SAE | CE1 | TYR- 204 | 3.79 | 0 | Hydrophobic |
| OAW | MG | MG- 403 | 2.13 | 0 | Metal Acceptor |
| OAV | MG | MG- 404 | 1.93 | 0 | Metal Acceptor |
| OAV | MG | MG- 405 | 2.28 | 0 | Metal Acceptor |
| OAZ | MG | MG- 405 | 2.07 | 0 | Metal Acceptor |
