sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.570 Å
X-ray
2013-06-21
| Name: | UDP-3-O-acyl-N-acetylglucosamine deacetylase |
|---|---|
| ID: | LPXC_PSEAE |
| AC: | P47205 |
| Organism: | Pseudomonas aeruginosa |
| Reign: | Bacteria |
| TaxID: | 208964 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 19.670 |
|---|---|
| Number of residues: | 38 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 1.387 | 1019.250 |
| % Hydrophobic | % Polar |
|---|---|
| 55.96 | 44.04 |
| According to VolSite | |
| HET Code: | 1WM |
|---|---|
| Formula: | C26H21N3O5 |
| Molecular weight: | 455.462 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 52.67 % |
| Polar Surface area: | 144.91 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 6 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| -25.9819 | -14.7852 | 6.41156 |
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 |
| C13 | CD1 | LEU- 18 | 4.03 | 0 | Hydrophobic |
| C24 | CD2 | LEU- 18 | 3.92 | 0 | Hydrophobic |
| C25 | CE | MET- 62 | 4.21 | 0 | Hydrophobic |
| O04 | OG1 | THR- 190 | 2.54 | 129.54 | H-Bond (Protein Donor) |
| C10 | CG2 | THR- 190 | 4.03 | 0 | Hydrophobic |
| C12 | CG1 | ILE- 197 | 4.26 | 0 | Hydrophobic |
| C14 | CD1 | ILE- 197 | 3.53 | 0 | Hydrophobic |
| C15 | CG2 | ILE- 197 | 3.6 | 0 | Hydrophobic |
| C24 | CD1 | LEU- 200 | 4.05 | 0 | Hydrophobic |
| C23 | CD | ARG- 201 | 4.3 | 0 | Hydrophobic |
| C19 | CB | VAL- 211 | 4.3 | 0 | Hydrophobic |
| C11 | CB | ALA- 214 | 4.11 | 0 | Hydrophobic |
| C15 | CB | ALA- 214 | 4.47 | 0 | Hydrophobic |
| C14 | CB | ALA- 214 | 4.14 | 0 | Hydrophobic |
| C18 | CG2 | VAL- 216 | 3.88 | 0 | Hydrophobic |
| O27 | NZ | LYS- 238 | 3 | 161.68 | H-Bond (Protein Donor) |
| O27 | OD2 | ASP- 241 | 2.91 | 163.78 | H-Bond (Ligand Donor) |
| O01 | ZN | ZN- 301 | 2.23 | 0 | Metal Acceptor |
| O04 | ZN | ZN- 301 | 2.08 | 0 | Metal Acceptor |
| O33 | O | HOH- 506 | 3.45 | 156.36 | H-Bond (Protein Donor) |
