sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
2007-05-21
| Name: | Poly(A) polymerase, putative |
|---|---|
| ID: | Q381M1_TRYB2 |
| AC: | Q381M1 |
| Organism: | Trypanosoma brucei brucei |
| Reign: | Eukaryota |
| TaxID: | 185431 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 28.570 |
|---|---|
| Number of residues: | 37 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.467 | 975.375 |
| % Hydrophobic | % Polar |
|---|---|
| 39.10 | 60.90 |
| According to VolSite | |
| HET Code: | UPU |
|---|---|
| Formula: | C18H22N4O14P |
| Molecular weight: | 549.359 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 49.3 % |
| Polar Surface area: | 266.59 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 14 |
| H-Bond Donors: | 6 |
| Rings: | 4 |
| Aromatic rings: | 0 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 3 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 25.6952 | 22.1523 | -51.4168 |
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 |
| C1'A | CE2 | PHE- 52 | 3.97 | 0 | Hydrophobic |
| C2'B | CE2 | PHE- 52 | 4.44 | 0 | Hydrophobic |
| C4'A | CE2 | PHE- 52 | 3.48 | 0 | Hydrophobic |
| C5'A | CB | ASP- 68 | 4.5 | 0 | Hydrophobic |
| O2'B | OD1 | ASP- 68 | 3.02 | 165.07 | H-Bond (Ligand Donor) |
| C1'B | CG2 | VAL- 124 | 4.47 | 0 | Hydrophobic |
| C1'B | CG2 | THR- 138 | 4.18 | 0 | Hydrophobic |
| O2A | ND2 | ASN- 147 | 3.15 | 155.52 | H-Bond (Protein Donor) |
| O2'A | OD1 | ASN- 147 | 2.67 | 162.22 | H-Bond (Ligand Donor) |
| C2'A | CG | TYR- 189 | 4.06 | 0 | Hydrophobic |
| C3'A | CB | TYR- 189 | 4.18 | 0 | Hydrophobic |
| O1 | MG | MG- 401 | 2.75 | 0 | Metal Acceptor |
