sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.500 Å
X-ray
2013-03-21
| Name: | Uridine kinase |
|---|---|
| ID: | URK_THET8 |
| AC: | Q5SKR5 |
| Organism: | Thermus thermophilus |
| Reign: | Bacteria |
| TaxID: | 300852 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 32.159 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 24 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | ACP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.097 | 624.375 |
| % Hydrophobic | % Polar |
|---|---|
| 32.97 | 67.03 |
| According to VolSite | |
| HET Code: | CTN |
|---|---|
| Formula: | C9H13N3O5 |
| Molecular weight: | 243.217 g/mol |
| DrugBank ID: | DB02097 |
| Buried Surface Area: | 79.66 % |
| Polar Surface area: | 128.61 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 4 |
| Rings: | 2 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| 24.5043 | -13.3336 | -2.50312 |
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 |
| C5' | CB | ASP- 40 | 4.03 | 0 | Hydrophobic |
| C2' | CB | TYR- 59 | 3.97 | 0 | Hydrophobic |
| O2' | OD2 | ASP- 60 | 2.63 | 166.16 | H-Bond (Ligand Donor) |
| O2' | OD1 | ASP- 60 | 3.41 | 134.46 | H-Bond (Ligand Donor) |
| O3' | OD1 | ASP- 60 | 2.72 | 154.35 | H-Bond (Ligand Donor) |
| N4 | OH | TYR- 88 | 2.76 | 166.24 | H-Bond (Ligand Donor) |
| N4 | ND1 | HIS- 93 | 3.23 | 171.19 | H-Bond (Ligand Donor) |
| C5' | CD1 | ILE- 113 | 4.06 | 0 | Hydrophobic |
| C3' | CD1 | ILE- 113 | 4.21 | 0 | Hydrophobic |
| O2' | NH2 | ARG- 142 | 2.93 | 154.89 | H-Bond (Protein Donor) |
| O2' | NH1 | ARG- 142 | 3.31 | 136.21 | H-Bond (Protein Donor) |
| O3' | NH1 | ARG- 142 | 2.91 | 141.48 | H-Bond (Protein Donor) |
| N3 | NH2 | ARG- 152 | 2.99 | 150.48 | H-Bond (Protein Donor) |
| O2 | NH2 | ARG- 152 | 3 | 136.75 | H-Bond (Protein Donor) |
| O2 | NH1 | ARG- 152 | 2.77 | 148.74 | H-Bond (Protein Donor) |
| O2 | NE2 | GLN- 160 | 3.31 | 169.63 | H-Bond (Protein Donor) |
