sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.200 Å
X-ray
2000-04-03
| Name: | 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 1 |
|---|---|
| ID: | F261_RAT |
| AC: | P07953 |
| Organism: | Rattus norvegicus |
| Reign: | Eukaryota |
| TaxID: | 10116 |
| EC Number: | 3.1.3.46 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 15 % |
| B | 85 % |
| B-Factor: | 18.874 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | GTP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.782 | 1407.375 |
| % Hydrophobic | % Polar |
|---|---|
| 38.85 | 61.15 |
| According to VolSite | |
| HET Code: | GTP |
|---|---|
| Formula: | C10H12N5O14P3 |
| Molecular weight: | 519.149 g/mol |
| DrugBank ID: | DB04137 |
| Buried Surface Area: | 57.79 % |
| Polar Surface area: | 335.56 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 17 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| -9.03684 | 15.8179 | 44.1302 |
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 |
| C2' | CG2 | ILE- 20 | 3.93 | 0 | Hydrophobic |
| C1' | CD1 | ILE- 20 | 4.14 | 0 | Hydrophobic |
| O5' | NH2 | ARG- 103 | 3.05 | 138.32 | H-Bond (Protein Donor) |
| C4' | CD | ARG- 103 | 4.39 | 0 | Hydrophobic |
| O1A | NZ | LYS- 107 | 2.89 | 145.36 | H-Bond (Protein Donor) |
| O1A | NZ | LYS- 107 | 2.89 | 0 | Ionic (Protein Cationic) |
| C3' | CE2 | TYR- 112 | 4.49 | 0 | Hydrophobic |
| O1G | NE2 | GLN- 144 | 3.38 | 153.56 | H-Bond (Protein Donor) |
| O1G | N | ALA- 145 | 3.48 | 135.3 | H-Bond (Protein Donor) |
| O3A | NH1 | ARG- 148 | 3.11 | 149.38 | H-Bond (Protein Donor) |
| O1A | CZ | ARG- 148 | 3.68 | 0 | Ionic (Protein Cationic) |
