sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.010 Å
X-ray
2011-10-14
| Name: | Peptide deformylase |
|---|---|
| ID: | DEF_STAAC |
| AC: | Q5HGZ3 |
| Organism: | Staphylococcus aureus |
| Reign: | Bacteria |
| TaxID: | 93062 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 21.137 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.124 | 317.250 |
| % Hydrophobic | % Polar |
|---|---|
| 37.23 | 62.77 |
| According to VolSite | |
| HET Code: | UDB |
|---|---|
| Formula: | C21H30F2N4O4 |
| Molecular weight: | 440.484 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 56.99 % |
| Polar Surface area: | 110.77 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 4 |
| Rings: | 2 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| -15.9944 | 144.911 | 46.7351 |
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 |
| CAA | CG | ARG- 56 | 3.8 | 0 | Hydrophobic |
| N | O | SER- 57 | 2.88 | 149.49 | H-Bond (Ligand Donor) |
| NAI | O | SER- 57 | 2.94 | 151.22 | H-Bond (Ligand Donor) |
| CAK | CB | SER- 57 | 4.48 | 0 | Hydrophobic |
| O | N | VAL- 59 | 3.04 | 150.77 | H-Bond (Protein Donor) |
| CAK | CG1 | VAL- 59 | 3.65 | 0 | Hydrophobic |
| CBA | CG2 | VAL- 59 | 3.96 | 0 | Hydrophobic |
| OAX | NE2 | GLN- 65 | 2.94 | 121.74 | H-Bond (Protein Donor) |
| F1 | CG | PRO- 78 | 4.02 | 0 | Hydrophobic |
| CBC | CD1 | LEU- 105 | 3.98 | 0 | Hydrophobic |
| CBC | CG | GLU- 109 | 3.87 | 0 | Hydrophobic |
| CBD | CB | GLU- 109 | 4.06 | 0 | Hydrophobic |
| CAA | CD2 | LEU- 112 | 3.78 | 0 | Hydrophobic |
| OAV | N | LEU- 112 | 2.81 | 168.38 | H-Bond (Protein Donor) |
| CBB | CG2 | VAL- 151 | 3.83 | 0 | Hydrophobic |
| CBB | CB | HIS- 154 | 4.09 | 0 | Hydrophobic |
| OAX | ZN | ZN- 350 | 2.18 | 0 | Metal Acceptor |
