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
2005-11-02
| 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: | 14.608 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.740 | 371.250 |
| % Hydrophobic | % Polar |
|---|---|
| 48.18 | 51.82 |
| According to VolSite | |
| HET Code: | Y12 |
|---|---|
| Formula: | C21H21NO5 |
| Molecular weight: | 367.395 g/mol |
| DrugBank ID: | DB08753 |
| Buried Surface Area: | 53.65 % |
| Polar Surface area: | 81.7 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 1 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| -79.0464 | -64.5937 | 50.3457 |
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 |
| C25 | CB | SER- 42 | 4.21 | 0 | Hydrophobic |
| O27 | N | ILE- 45 | 2.78 | 167.81 | H-Bond (Protein Donor) |
| C4 | CD1 | ILE- 45 | 3.58 | 0 | Hydrophobic |
| O27 | N | GLY- 46 | 3.36 | 143.03 | H-Bond (Protein Donor) |
| C6 | CB | GLU- 94 | 4.05 | 0 | Hydrophobic |
| C1 | CG | GLU- 94 | 3.39 | 0 | Hydrophobic |
| N9 | O | GLY- 95 | 3.13 | 172.46 | H-Bond (Ligand Donor) |
| C18 | CD2 | LEU- 97 | 3.25 | 0 | Hydrophobic |
| C16 | CB | PRO- 100 | 4.17 | 0 | Hydrophobic |
| C3 | CD1 | LEU- 131 | 3.55 | 0 | Hydrophobic |
| C2 | CG1 | VAL- 134 | 3.86 | 0 | Hydrophobic |
| C4 | CB | ALA- 135 | 3.8 | 0 | Hydrophobic |
| C6 | CB | HIS- 138 | 4.2 | 0 | Hydrophobic |
