sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.350 Å
X-ray
2007-09-24
| Name: | 1-deoxypentalenic acid 11-beta-hydroxylase |
|---|---|
| ID: | PTLH_STRAW |
| AC: | Q82IZ1 |
| Organism: | Streptomyces avermitilis |
| Reign: | Bacteria |
| TaxID: | 227882 |
| EC Number: | 1.14.11.35 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 8.670 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 29 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | FE |
| Ligandability | Volume (Å3) |
|---|---|
| 0.555 | 766.125 |
| % Hydrophobic | % Polar |
|---|---|
| 45.37 | 54.63 |
| According to VolSite | |
| HET Code: | 1PL |
|---|---|
| Formula: | C15H21O2 |
| Molecular weight: | 233.326 g/mol |
| DrugBank ID: | DB06903 |
| Buried Surface Area: | 67.51 % |
| Polar Surface area: | 40.12 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 0 |
| Rings: | 3 |
| Aromatic rings: | 0 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 1 |
| X | Y | Z |
|---|---|---|
| 23.6329 | 30.4604 | 2.78129 |
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 |
| O1 | NH2 | ARG- 117 | 3.4 | 135.89 | H-Bond (Protein Donor) |
| O1 | NH1 | ARG- 117 | 3.08 | 149.49 | H-Bond (Protein Donor) |
| O2 | NH2 | ARG- 117 | 2.84 | 168.02 | H-Bond (Protein Donor) |
| O1 | CZ | ARG- 117 | 3.67 | 0 | Ionic (Protein Cationic) |
| O2 | CZ | ARG- 117 | 3.78 | 0 | Ionic (Protein Cationic) |
| C11 | CB | THR- 134 | 4.23 | 0 | Hydrophobic |
| C12 | CG2 | THR- 134 | 3.79 | 0 | Hydrophobic |
| C10 | CB | HIS- 137 | 4.31 | 0 | Hydrophobic |
| C11 | CB | HIS- 137 | 4.47 | 0 | Hydrophobic |
| C10 | CD2 | PHE- 141 | 4.22 | 0 | Hydrophobic |
| C10 | CD2 | TYR- 142 | 3.88 | 0 | Hydrophobic |
| C3 | CD2 | TYR- 142 | 3.74 | 0 | Hydrophobic |
| C15 | CE1 | TYR- 142 | 3.84 | 0 | Hydrophobic |
| C5 | CE2 | TYR- 142 | 3.97 | 0 | Hydrophobic |
| C14 | CD1 | TYR- 142 | 4.25 | 0 | Hydrophobic |
| O1 | NH2 | ARG- 188 | 2.98 | 163.8 | H-Bond (Protein Donor) |
| O1 | CZ | ARG- 188 | 3.88 | 0 | Ionic (Protein Cationic) |
| C1 | CG | ARG- 188 | 4.25 | 0 | Hydrophobic |
| C9 | CG2 | VAL- 193 | 4.45 | 0 | Hydrophobic |
| C8 | CG1 | VAL- 193 | 4.1 | 0 | Hydrophobic |
| C14 | CB | ALA- 269 | 3.87 | 0 | Hydrophobic |
| C14 | CB | SER- 270 | 4.42 | 0 | Hydrophobic |
| C1 | CB | SER- 270 | 4.31 | 0 | Hydrophobic |
| C3 | CD1 | ILE- 273 | 4.35 | 0 | Hydrophobic |
| C14 | CG2 | ILE- 273 | 3.93 | 0 | Hydrophobic |
| C10 | CD1 | ILE- 273 | 4.36 | 0 | Hydrophobic |
