sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.310 Å
X-ray
2012-08-15
| Name: | Yersiniabactin biosynthetic protein YbtU |
|---|---|
| ID: | A1JTG0_YERE8 |
| AC: | A1JTG0 |
| Organism: | Yersinia enterocolitica serotype O:8 / biotype 1B |
| Reign: | Bacteria |
| TaxID: | 393305 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| C | 2 % |
| D | 98 % |
| B-Factor: | 27.673 |
|---|---|
| Number of residues: | 45 |
| Including | |
| Standard Amino Acids: | 45 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.822 | 1751.625 |
| % Hydrophobic | % Polar |
|---|---|
| 50.87 | 49.13 |
| According to VolSite | |
| HET Code: | NAP |
|---|---|
| Formula: | C21H25N7O17P3 |
| Molecular weight: | 740.381 g/mol |
| DrugBank ID: | DB03461 |
| Buried Surface Area: | 60.38 % |
| Polar Surface area: | 405.54 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 21 |
| H-Bond Donors: | 5 |
| Rings: | 5 |
| Aromatic rings: | 3 |
| Anionic atoms: | 4 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 13 |
| X | Y | Z |
|---|---|---|
| -65.303 | -1.54463 | -50.0188 |
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 |
| O3B | N | ALA- 15 | 2.73 | 139.31 | H-Bond (Protein Donor) |
| C5B | CB | LYS- 16 | 3.86 | 0 | Hydrophobic |
| O1N | N | PHE- 17 | 2.82 | 163.94 | H-Bond (Protein Donor) |
| C5N | CB | PHE- 17 | 4.22 | 0 | Hydrophobic |
| C5D | CB | PHE- 17 | 4.05 | 0 | Hydrophobic |
| DuAr | DuAr | PHE- 17 | 3.76 | 0 | Aromatic Face/Face |
| O2B | N | GLN- 40 | 3.34 | 164.35 | H-Bond (Protein Donor) |
| O2X | N | SER- 42 | 3.43 | 154.49 | H-Bond (Protein Donor) |
| C4D | CG1 | VAL- 73 | 3.88 | 0 | Hydrophobic |
| C1B | CG2 | VAL- 74 | 4.33 | 0 | Hydrophobic |
| O2A | N | ARG- 75 | 2.67 | 173.19 | H-Bond (Protein Donor) |
| C3D | CG | ARG- 75 | 3.81 | 0 | Hydrophobic |
| C4D | CG | GLU- 100 | 4.07 | 0 | Hydrophobic |
| C2D | CG | GLU- 100 | 4.47 | 0 | Hydrophobic |
| N7N | OE2 | GLU- 100 | 3.16 | 151.88 | H-Bond (Ligand Donor) |
| O2D | O | HIS- 101 | 2.97 | 163.45 | H-Bond (Ligand Donor) |
| O7N | OH | TYR- 128 | 2.61 | 147.2 | H-Bond (Protein Donor) |
