sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.660 Å
X-ray
2012-03-20
| Name: | Peptide deformylase |
|---|---|
| ID: | Q672W7_HELPX |
| AC: | Q672W7 |
| Organism: | Helicobacter pylori |
| Reign: | Bacteria |
| TaxID: | 210 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 24.428 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.857 | 411.750 |
| % Hydrophobic | % Polar |
|---|---|
| 54.92 | 45.08 |
| According to VolSite | |
| HET Code: | QAP |
|---|---|
| Formula: | C17H16O4 |
| Molecular weight: | 284.307 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 65.03 % |
| Polar Surface area: | 66.76 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 77.9957 | 89.45 | 51.7596 |
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 |
| C3 | CG1 | ILE- 45 | 4.07 | 0 | Hydrophobic |
| C8 | CD1 | ILE- 45 | 3.98 | 0 | Hydrophobic |
| O4 | N | ILE- 45 | 2.85 | 154.37 | H-Bond (Protein Donor) |
| O4 | N | GLY- 46 | 3.38 | 155.77 | H-Bond (Protein Donor) |
| C9 | CG | GLU- 94 | 4.2 | 0 | Hydrophobic |
| C7 | CB | GLU- 94 | 3.63 | 0 | Hydrophobic |
| C11 | CD2 | LEU- 97 | 3.29 | 0 | Hydrophobic |
| C15 | CB | PRO- 100 | 4.37 | 0 | Hydrophobic |
| O2 | N | GLY- 101 | 2.75 | 159.71 | H-Bond (Protein Donor) |
| C8 | CD1 | LEU- 131 | 3.47 | 0 | Hydrophobic |
| C8 | CG1 | VAL- 134 | 4.02 | 0 | Hydrophobic |
| C5 | CB | ALA- 135 | 3.83 | 0 | Hydrophobic |
| C1 | CB | HIS- 138 | 4.42 | 0 | Hydrophobic |
