sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.940 Å
X-ray
2005-12-05
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.710 | 7.500 | 7.340 | 0.710 | 8.440 | 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 |
|---|---|
| F | 100 % |
| B-Factor: | 29.473 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 3 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | ZN ZN ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.144 | 816.750 |
| % Hydrophobic | % Polar |
|---|---|
| 38.43 | 61.57 |
| According to VolSite | |
| HET Code: | BFQ |
|---|---|
| Formula: | C9H20NO7P2 |
| Molecular weight: | 316.205 g/mol |
| DrugBank ID: | DB00710 |
| Buried Surface Area: | 65.49 % |
| Polar Surface area: | 170.67 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 2 |
| Rings: | 0 |
| Aromatic rings: | 0 |
| Anionic atoms: | 4 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| 15.6973 | 78.9309 | 25.3524 |
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 |
| C32 | CB | PHE- 99 | 3.81 | 0 | Hydrophobic |
| C16 | CD2 | LEU- 100 | 4.02 | 0 | Hydrophobic |
| C16 | CB | ASP- 103 | 4.42 | 0 | Hydrophobic |
| C29 | CB | ASP- 103 | 3.87 | 0 | Hydrophobic |
| C35 | CB | ASP- 103 | 4.11 | 0 | Hydrophobic |
| C35 | CE | MET- 106 | 4.33 | 0 | Hydrophobic |
| O2 | NH2 | ARG- 112 | 3.15 | 140.43 | H-Bond (Protein Donor) |
| O5 | NH1 | ARG- 112 | 2.65 | 159.97 | H-Bond (Protein Donor) |
| O5 | NH2 | ARG- 112 | 3.15 | 131.86 | H-Bond (Protein Donor) |
| O5 | CZ | ARG- 112 | 3.33 | 0 | Ionic (Protein Cationic) |
| C26 | CG2 | THR- 167 | 3.98 | 0 | Hydrophobic |
| C32 | CG2 | THR- 167 | 3.97 | 0 | Hydrophobic |
| C32 | CB | GLN- 171 | 4.13 | 0 | Hydrophobic |
| C35 | CG | GLN- 171 | 4.19 | 0 | Hydrophobic |
| O10 | NZ | LYS- 200 | 2.67 | 151.49 | H-Bond (Protein Donor) |
| O10 | NZ | LYS- 200 | 2.67 | 0 | Ionic (Protein Cationic) |
| O12 | NZ | LYS- 200 | 3.7 | 0 | Ionic (Protein Cationic) |
| O14 | OD2 | ASP- 243 | 3 | 171.6 | H-Bond (Ligand Donor) |
| O3 | NZ | LYS- 257 | 3.53 | 0 | Ionic (Protein Cationic) |
| O5 | NZ | LYS- 257 | 3.68 | 0 | Ionic (Protein Cationic) |
| O2 | ZN | ZN- 1001 | 1.97 | 0 | Metal Acceptor |
| O9 | ZN | ZN- 1001 | 2.22 | 0 | Metal Acceptor |
| O3 | ZN | ZN- 1002 | 1.96 | 0 | Metal Acceptor |
| O12 | ZN | ZN- 1002 | 2.04 | 0 | Metal Acceptor |
| O9 | ZN | ZN- 1003 | 2.1 | 0 | Metal Acceptor |
