sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
2007-03-07
| Name: | Acetyl-coenzyme A synthetase |
|---|---|
| ID: | ACSA_SALTY |
| AC: | Q8ZKF6 |
| Organism: | Salmonella typhimurium |
| Reign: | Bacteria |
| TaxID: | 99287 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 27.692 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 2 |
| Cofactors: | COA |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.088 | 762.750 |
| % Hydrophobic | % Polar |
|---|---|
| 45.58 | 54.42 |
| According to VolSite | |
| HET Code: | PRX |
|---|---|
| Formula: | C13H19N5O7P |
| Molecular weight: | 388.293 g/mol |
| DrugBank ID: | DB03230 |
| Buried Surface Area: | 71.39 % |
| Polar Surface area: | 187.7 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 11 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| -35.0692 | 66.4366 | 24.0616 |
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 |
| C2P | CG1 | VAL- 310 | 3.84 | 0 | Hydrophobic |
| C3P | CG2 | VAL- 386 | 3.7 | 0 | Hydrophobic |
| N7 | N | GLY- 387 | 3.23 | 138.6 | H-Bond (Protein Donor) |
| N6 | OD1 | ASP- 411 | 2.94 | 144.17 | H-Bond (Ligand Donor) |
| N6 | O | THR- 412 | 2.85 | 152 | H-Bond (Ligand Donor) |
| C3P | CE2 | TRP- 414 | 3.59 | 0 | Hydrophobic |
| C5' | CB | GLN- 415 | 3.88 | 0 | Hydrophobic |
| C3' | CG | GLN- 415 | 3.94 | 0 | Hydrophobic |
| O3' | NE2 | GLN- 415 | 2.83 | 169.69 | H-Bond (Protein Donor) |
| O1P | N | THR- 416 | 2.86 | 155.89 | H-Bond (Protein Donor) |
| O2' | OD1 | ASP- 500 | 2.62 | 158.97 | H-Bond (Ligand Donor) |
| O3' | OD1 | ASP- 500 | 3.37 | 149.86 | H-Bond (Ligand Donor) |
| O3' | NH1 | ARG- 515 | 2.9 | 143.44 | H-Bond (Protein Donor) |
| C2' | CD | ARG- 515 | 4.48 | 0 | Hydrophobic |
| C5' | CD | ARG- 526 | 4.17 | 0 | Hydrophobic |
| O1P | CZ | ARG- 526 | 3.91 | 0 | Ionic (Protein Cationic) |
| O1P | NH1 | ARG- 526 | 2.84 | 138.02 | H-Bond (Protein Donor) |
