sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.250 Å
X-ray
2006-12-02
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 5.700 | 5.700 | 5.700 | 0.000 | 5.700 | 1 |
| Name: | UDP-3-O-acyl-N-acetylglucosamine deacetylase |
|---|---|
| ID: | LPXC_AQUAE |
| AC: | O67648 |
| Organism: | Aquifex aeolicus |
| Reign: | Bacteria |
| TaxID: | 224324 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 14 % |
| B | 86 % |
| B-Factor: | 30.643 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.162 | 1333.125 |
| % Hydrophobic | % Polar |
|---|---|
| 49.37 | 50.63 |
| According to VolSite | |
| HET Code: | AI7 |
|---|---|
| Formula: | C14H19O3 |
| Molecular weight: | 235.299 g/mol |
| DrugBank ID: | DB07355 |
| Buried Surface Area: | 60.9 % |
| Polar Surface area: | 49.36 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 0 |
| Rings: | 1 |
| Aromatic rings: | 1 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 59.7449 | 65.9148 | -14.1881 |
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 |
| C12 | CD1 | ILE- 18 | 3.67 | 0 | Hydrophobic |
| C9 | CB | HIS- 58 | 4.2 | 0 | Hydrophobic |
| C10 | CG2 | THR- 191 | 4.18 | 0 | Hydrophobic |
| C12 | CG2 | THR- 191 | 4.48 | 0 | Hydrophobic |
| C4 | CB | ALA- 193 | 4.44 | 0 | Hydrophobic |
| C8 | CD1 | ILE- 198 | 4.28 | 0 | Hydrophobic |
| C11 | CD1 | ILE- 198 | 4.05 | 0 | Hydrophobic |
| C4 | CD1 | ILE- 201 | 3.57 | 0 | Hydrophobic |
| O17 | NZ | LYS- 202 | 2.51 | 160.22 | H-Bond (Protein Donor) |
| O17 | NZ | LYS- 202 | 2.51 | 0 | Ionic (Protein Cationic) |
| C2 | CD2 | LEU- 212 | 3.92 | 0 | Hydrophobic |
| C6 | CG2 | THR- 215 | 4.2 | 0 | Hydrophobic |
| C7 | CB | THR- 215 | 4.34 | 0 | Hydrophobic |
| C7 | CG2 | VAL- 217 | 3.55 | 0 | Hydrophobic |
