sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.800 Å
X-ray
2013-09-19
| Name: | 3-oxoacyl-ACP synthase |
|---|---|
| ID: | I6Y8T4_MYCTU |
| AC: | I6Y8T4 |
| Organism: | Mycobacterium tuberculosis |
| Reign: | Bacteria |
| TaxID: | 83332 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 20.829 |
|---|---|
| Number of residues: | 37 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.600 | 526.500 |
| % Hydrophobic | % Polar |
|---|---|
| 62.18 | 37.82 |
| According to VolSite | |
| HET Code: | 7RD |
|---|---|
| Formula: | C14H18N3O2S |
| Molecular weight: | 292.377 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 77.91 % |
| Polar Surface area: | 115.18 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 0 |
| Rings: | 1 |
| Aromatic rings: | 0 |
| Anionic atoms: | 2 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| -6.9053 | -25.4321 | 42.0879 |
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 |
| N | NE2 | GLN- 171 | 2.87 | 154.58 | H-Bond (Protein Donor) |
| S | CB | GLN- 171 | 4.42 | 0 | Hydrophobic |
| C11 | CE1 | PHE- 237 | 3.73 | 0 | Hydrophobic |
| C10 | CD1 | PHE- 237 | 3.77 | 0 | Hydrophobic |
| C6 | CG | PRO- 280 | 3.83 | 0 | Hydrophobic |
| C3 | CB | PRO- 280 | 4.02 | 0 | Hydrophobic |
| O | NE2 | HIS- 311 | 2.86 | 165.39 | H-Bond (Protein Donor) |
| C9 | CG2 | THR- 313 | 3.66 | 0 | Hydrophobic |
| C9 | CG2 | THR- 315 | 4.19 | 0 | Hydrophobic |
| O | NE2 | HIS- 345 | 2.79 | 165.86 | H-Bond (Protein Donor) |
| S | CB | PHE- 402 | 4.09 | 0 | Hydrophobic |
| C6 | CB | PHE- 402 | 4.5 | 0 | Hydrophobic |
| C3 | CB | PHE- 402 | 3.8 | 0 | Hydrophobic |
| C11 | CZ | PHE- 404 | 3.53 | 0 | Hydrophobic |
| C10 | CE1 | PHE- 404 | 4.02 | 0 | Hydrophobic |
| C5 | CE1 | PHE- 404 | 4.39 | 0 | Hydrophobic |
