sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.470 Å
X-ray
2010-01-13
| Name: | Farnesyl pyrophosphate synthase, putative |
|---|---|
| ID: | A5K4U6_PLAVS |
| AC: | A5K4U6 |
| Organism: | Plasmodium vivax |
| Reign: | Eukaryota |
| TaxID: | 126793 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 25.893 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 23 |
| Non Standard Amino Acids: | 4 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | MG MG MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.901 | 1181.250 |
| % Hydrophobic | % Polar |
|---|---|
| 45.43 | 54.57 |
| According to VolSite | |
| HET Code: | ZOL |
|---|---|
| Formula: | C5H6N2O7P2 |
| Molecular weight: | 268.058 g/mol |
| DrugBank ID: | DB00399 |
| Buried Surface Area: | 67.16 % |
| 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 |
|---|---|---|
| -9.84987 | 15.5481 | -36.2998 |
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- 123 | 4.1 | 0 | Hydrophobic |
| O17 | NH1 | ARG- 135 | 3.35 | 158.46 | H-Bond (Protein Donor) |
| O15 | NH1 | ARG- 135 | 3.48 | 120.78 | H-Bond (Protein Donor) |
| O15 | CZ | ARG- 135 | 3.4 | 0 | Ionic (Protein Cationic) |
| O10 | NZ | LYS- 243 | 2.54 | 168.27 | H-Bond (Protein Donor) |
| O10 | NZ | LYS- 243 | 2.54 | 0 | Ionic (Protein Cationic) |
| O13 | OD1 | ASP- 287 | 2.82 | 161.07 | H-Bond (Ligand Donor) |
| O16 | NZ | LYS- 301 | 3.38 | 0 | Ionic (Protein Cationic) |
| O15 | NZ | LYS- 301 | 2.74 | 0 | Ionic (Protein Cationic) |
| O15 | NZ | LYS- 301 | 2.74 | 150.46 | H-Bond (Protein Donor) |
| O17 | MG | MG- 1102 | 2.01 | 0 | Metal Acceptor |
| O12 | MG | MG- 1102 | 2.14 | 0 | Metal Acceptor |
| O12 | MG | MG- 1103 | 2.22 | 0 | Metal Acceptor |
| O16 | MG | MG- 1104 | 2.03 | 0 | Metal Acceptor |
| O11 | MG | MG- 1104 | 1.98 | 0 | Metal Acceptor |
