sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.170 Å
X-ray
2013-05-21
| Name: | 3-oxoacyl-[ACP] synthase III |
|---|---|
| ID: | Q8PDX2_XANCP |
| AC: | Q8PDX2 |
| Organism: | Xanthomonas campestris pv. campestris |
| Reign: | Bacteria |
| TaxID: | 190485 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 4 % |
| B | 96 % |
| B-Factor: | 39.601 |
|---|---|
| Number of residues: | 57 |
| Including | |
| Standard Amino Acids: | 55 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.640 | 897.750 |
| % Hydrophobic | % Polar |
|---|---|
| 63.53 | 36.47 |
| According to VolSite | |
| HET Code: | DCC |
|---|---|
| Formula: | C33H54N7O17P3S |
| Molecular weight: | 945.805 g/mol |
| DrugBank ID: | DB03264 |
| Buried Surface Area: | 57.26 % |
| Polar Surface area: | 429.68 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 22 |
| H-Bond Donors: | 5 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 30 |
| X | Y | Z |
|---|---|---|
| -10.1423 | 14.2852 | -41.8353 |
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 |
| C1' | CG2 | VAL- 62 | 3.81 | 0 | Hydrophobic |
| CP7 | CG1 | VAL- 62 | 3.65 | 0 | Hydrophobic |
| C4' | CG2 | VAL- 66 | 4.28 | 0 | Hydrophobic |
| CP7 | CG1 | VAL- 66 | 3.51 | 0 | Hydrophobic |
| CP7 | CB | ALA- 67 | 4.08 | 0 | Hydrophobic |
| C11 | CG1 | VAL- 111 | 4.43 | 0 | Hydrophobic |
| CA9 | CG1 | VAL- 111 | 4.43 | 0 | Hydrophobic |
| CA5 | CG2 | VAL- 111 | 3.74 | 0 | Hydrophobic |
| CA3 | CG | GLU- 117 | 4.02 | 0 | Hydrophobic |
| CA7 | CG | GLU- 171 | 4.06 | 0 | Hydrophobic |
| CA8 | CB | GLU- 171 | 4.24 | 0 | Hydrophobic |
| C10 | CB | ALA- 173 | 4.35 | 0 | Hydrophobic |
| C12 | CB | VAL- 176 | 4.14 | 0 | Hydrophobic |
| N6 | O | ARG- 195 | 3.21 | 155.43 | H-Bond (Ligand Donor) |
| O2' | NH1 | ARG- 195 | 3.18 | 129.64 | H-Bond (Protein Donor) |
| CP4 | CB | ALA- 199 | 3.51 | 0 | Hydrophobic |
| CP4 | CG2 | THR- 202 | 4.02 | 0 | Hydrophobic |
| S | CD2 | LEU- 203 | 4 | 0 | Hydrophobic |
| CA2 | CD2 | LEU- 203 | 3.69 | 0 | Hydrophobic |
| CA6 | CD2 | LEU- 203 | 4.09 | 0 | Hydrophobic |
| CP1 | SG | CYS- 239 | 3.95 | 0 | Hydrophobic |
| C12 | CD1 | LEU- 243 | 4.23 | 0 | Hydrophobic |
| S | CE | MET- 246 | 3.64 | 0 | Hydrophobic |
| CA2 | SD | MET- 246 | 4.07 | 0 | Hydrophobic |
| CP1 | CG2 | THR- 248 | 4.02 | 0 | Hydrophobic |
| N6 | OG1 | THR- 250 | 2.96 | 154.15 | H-Bond (Ligand Donor) |
| CP9 | CB | THR- 250 | 4.13 | 0 | Hydrophobic |
| CP4 | CG2 | THR- 250 | 4.2 | 0 | Hydrophobic |
| O12 | CZ | ARG- 251 | 3.45 | 0 | Ionic (Protein Cationic) |
| O22 | CZ | ARG- 251 | 3.78 | 0 | Ionic (Protein Cationic) |
| CP1 | CD1 | LEU- 253 | 3.76 | 0 | Hydrophobic |
| NP1 | O | HOH- 605 | 2.69 | 147.04 | H-Bond (Ligand Donor) |
