sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.760 Å
X-ray
2012-02-06
| Name: | Deoxyuridine triphosphatase, putative |
|---|---|
| ID: | Q57ZH3_TRYB2 |
| AC: | Q57ZH3 |
| Organism: | Trypanosoma brucei brucei |
| Reign: | Eukaryota |
| TaxID: | 185431 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 17.968 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 4 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | MG MG MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.333 | 459.000 |
| % Hydrophobic | % Polar |
|---|---|
| 52.21 | 47.79 |
| According to VolSite | |
| HET Code: | UMP |
|---|---|
| Formula: | C9H11N2O8P |
| Molecular weight: | 306.166 g/mol |
| DrugBank ID: | DB03800 |
| Buried Surface Area: | 63.33 % |
| Polar Surface area: | 161.1 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 0 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| -3.33125 | 18.9137 | 21.4919 |
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 |
| O2 | NE2 | GLN- 21 | 2.97 | 155.23 | H-Bond (Protein Donor) |
| N3 | OD1 | ASN- 25 | 2.75 | 172.62 | H-Bond (Ligand Donor) |
| C3' | CB | ASP- 79 | 4.02 | 0 | Hydrophobic |
| O3' | OD1 | ASP- 79 | 2.72 | 164.43 | H-Bond (Ligand Donor) |
| C2' | CB | HIS- 82 | 3.44 | 0 | Hydrophobic |
| C3' | CE2 | PHE- 83 | 3.98 | 0 | Hydrophobic |
| C2' | CZ | PHE- 83 | 3.67 | 0 | Hydrophobic |
| C5' | CZ | PHE- 83 | 4.17 | 0 | Hydrophobic |
| O3' | ND2 | ASN- 212 | 2.98 | 157.63 | H-Bond (Protein Donor) |
| OP1 | NH1 | ARG- 215 | 3.03 | 138.88 | H-Bond (Protein Donor) |
| OP1 | CZ | ARG- 215 | 3.97 | 0 | Ionic (Protein Cationic) |
| OP3 | OH | TYR- 220 | 2.56 | 172.44 | H-Bond (Protein Donor) |
| OP1 | NZ | LYS- 227 | 3.18 | 0 | Ionic (Protein Cationic) |
| OP2 | MG | MG- 303 | 1.92 | 0 | Metal Acceptor |
| O5' | O | HOH- 409 | 3.11 | 179.97 | H-Bond (Protein Donor) |
