sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.700 Å
X-ray
2005-07-29
| Name: | Peptide deformylase |
|---|---|
| ID: | DEF_STRR6 |
| AC: | Q8DP79 |
| Organism: | Streptococcus pneumoniae |
| Reign: | Bacteria |
| TaxID: | 171101 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 25.818 |
|---|---|
| Number of residues: | 26 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.422 | 307.125 |
| % Hydrophobic | % Polar |
|---|---|
| 37.36 | 62.64 |
| According to VolSite | |
| HET Code: | SB8 |
|---|---|
| Formula: | C16H15NO4 |
| Molecular weight: | 285.295 g/mol |
| DrugBank ID: | DB08524 |
| Buried Surface Area: | 68.75 % |
| Polar Surface area: | 66.84 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 1 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -5.36881 | 25.7246 | -0.991286 |
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 |
| C4 | CG2 | VAL- 70 | 3.76 | 0 | Hydrophobic |
| O32 | NE2 | GLN- 76 | 3.35 | 148.34 | H-Bond (Protein Donor) |
| C1 | CD1 | LEU- 123 | 4.05 | 0 | Hydrophobic |
| C14 | CD1 | LEU- 123 | 3.35 | 0 | Hydrophobic |
| C13 | CD1 | LEU- 123 | 3.48 | 0 | Hydrophobic |
| C13 | CB | GLU- 125 | 4.35 | 0 | Hydrophobic |
| C1 | CG | GLU- 128 | 3.91 | 0 | Hydrophobic |
| O8 | N | GLY- 129 | 2.65 | 144 | H-Bond (Protein Donor) |
| O32 | N | LEU- 131 | 2.68 | 162.72 | H-Bond (Protein Donor) |
| C11 | CE1 | TYR- 166 | 3.42 | 0 | Hydrophobic |
| C6 | CG2 | ILE- 169 | 4.21 | 0 | Hydrophobic |
| C5 | CG1 | VAL- 170 | 4.16 | 0 | Hydrophobic |
| C6 | CG2 | VAL- 170 | 3.77 | 0 | Hydrophobic |
| C5 | CB | HIS- 173 | 3.58 | 0 | Hydrophobic |
| O35 | OE1 | GLU- 174 | 2.68 | 154.01 | H-Bond (Protein Donor) |
