sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.250 Å
X-ray
2003-08-13
| Name: | FKBP-type peptidyl-prolyl cis-trans isomerase FkpA |
|---|---|
| ID: | FKBA_ECOLI |
| AC: | P45523 |
| Organism: | Escherichia coli |
| Reign: | Bacteria |
| TaxID: | 83333 |
| EC Number: | 5.2.1.8 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 24.920 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 24 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.483 | 273.375 |
| % Hydrophobic | % Polar |
|---|---|
| 49.38 | 50.62 |
| According to VolSite | |
| HET Code: | FK5 |
|---|---|
| Formula: | C44H69NO12 |
| Molecular weight: | 804.018 g/mol |
| DrugBank ID: | DB00864 |
| Buried Surface Area: | 32.41 % |
| Polar Surface area: | 178.36 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 12 |
| H-Bond Donors: | 3 |
| Rings: | 4 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 12.4904 | 24.4882 | 23.0161 |
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 |
| C5 | CZ | TYR- 146 | 3.68 | 0 | Hydrophobic |
| C35 | CD1 | PHE- 156 | 4.4 | 0 | Hydrophobic |
| O6 | OD2 | ASP- 157 | 2.9 | 167.97 | H-Bond (Ligand Donor) |
| C5 | CD2 | LEU- 166 | 3.93 | 0 | Hydrophobic |
| C44 | CD1 | LEU- 166 | 4.09 | 0 | Hydrophobic |
| C4 | CE2 | PHE- 168 | 4.23 | 0 | Hydrophobic |
| C4 | CG1 | VAL- 173 | 4.27 | 0 | Hydrophobic |
| C26 | CG1 | VAL- 173 | 4.22 | 0 | Hydrophobic |
| C41 | CG1 | VAL- 173 | 4 | 0 | Hydrophobic |
| C3 | CG1 | ILE- 174 | 4.1 | 0 | Hydrophobic |
| C30 | CG2 | ILE- 174 | 3.95 | 0 | Hydrophobic |
| C45 | CG2 | ILE- 174 | 4.34 | 0 | Hydrophobic |
| O2 | N | ILE- 174 | 2.8 | 154.94 | H-Bond (Protein Donor) |
| C5 | CZ2 | TRP- 177 | 4.09 | 0 | Hydrophobic |
| C3 | CE2 | TRP- 177 | 3.38 | 0 | Hydrophobic |
| C11 | CZ | TYR- 200 | 4.15 | 0 | Hydrophobic |
| C30 | CE1 | TYR- 200 | 4.3 | 0 | Hydrophobic |
| C35 | CE2 | TYR- 200 | 3.94 | 0 | Hydrophobic |
| C45 | CD1 | TYR- 200 | 3.9 | 0 | Hydrophobic |
| C35 | CG2 | VAL- 205 | 4.27 | 0 | Hydrophobic |
| C35 | CD1 | ILE- 208 | 3.63 | 0 | Hydrophobic |
