sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.190 Å
X-ray
2006-08-31
| Name: | D-alanine--D-alanine ligase |
|---|---|
| ID: | DDL_STAAC |
| AC: | Q5HEB7 |
| Organism: | Staphylococcus aureus |
| Reign: | Bacteria |
| TaxID: | 93062 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 41.627 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.086 | 270.000 |
| % Hydrophobic | % Polar |
|---|---|
| 63.75 | 36.25 |
| According to VolSite | |
| HET Code: | G1L |
|---|---|
| Formula: | C12H13ClF3NO |
| Molecular weight: | 279.686 g/mol |
| DrugBank ID: | DB07805 |
| Buried Surface Area: | 75.83 % |
| Polar Surface area: | 29.1 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 1 |
| H-Bond Donors: | 1 |
| Rings: | 1 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 16.5461 | -2.83856 | -0.450167 |
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 |
| C14 | CG1 | VAL- 19 | 4.43 | 0 | Hydrophobic |
| C15 | CG1 | VAL- 19 | 3.95 | 0 | Hydrophobic |
| C15 | CB | SER- 20 | 4.36 | 0 | Hydrophobic |
| C15 | CB | THR- 23 | 4.42 | 0 | Hydrophobic |
| F21 | CD1 | PHE- 92 | 3.46 | 0 | Hydrophobic |
| F21 | CD2 | LEU- 94 | 4.08 | 0 | Hydrophobic |
| C2 | CD2 | LEU- 94 | 3.37 | 0 | Hydrophobic |
| CL17 | CB | HIS- 96 | 4.46 | 0 | Hydrophobic |
| F21 | CB | VAL- 117 | 3.62 | 0 | Hydrophobic |
| F23 | CG1 | VAL- 117 | 3.32 | 0 | Hydrophobic |
| F23 | CD2 | LEU- 289 | 3.23 | 0 | Hydrophobic |
| C4 | CD1 | LEU- 289 | 3.66 | 0 | Hydrophobic |
| F22 | CE | MET- 310 | 4.14 | 0 | Hydrophobic |
| C2 | CE | MET- 310 | 4.39 | 0 | Hydrophobic |
| C1 | CB | MET- 310 | 4.3 | 0 | Hydrophobic |
| CL17 | CB | MET- 310 | 3.91 | 0 | Hydrophobic |
| C5 | CG | PRO- 311 | 4.27 | 0 | Hydrophobic |
| N11 | O | PRO- 311 | 2.95 | 150.09 | H-Bond (Ligand Donor) |
| C5 | CB | PHE- 313 | 3.81 | 0 | Hydrophobic |
| F23 | CD2 | LEU- 337 | 3.96 | 0 | Hydrophobic |
