sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
2010-06-08
| Name: | DNA-directed DNA polymerase |
|---|---|
| ID: | DPOL_BPR69 |
| AC: | Q38087 |
| Organism: | Enterobacteria phage RB69 |
| Reign: | Viruses |
| TaxID: | 12353 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 30.805 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 3 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | CA CA CA |
| Ligandability | Volume (Å3) |
|---|---|
| 0.144 | 992.250 |
| % Hydrophobic | % Polar |
|---|---|
| 30.61 | 69.39 |
| According to VolSite | |
| HET Code: | DCP |
|---|---|
| Formula: | C9H12N3O13P3 |
| Molecular weight: | 463.125 g/mol |
| DrugBank ID: | DB03258 |
| Buried Surface Area: | 52.47 % |
| Polar Surface area: | 288.71 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 15 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 0 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| -1.24514 | -8.57743 | 48.2019 |
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 | SER- 414 | 3.49 | 121.22 | H-Bond (Protein Donor) |
| O2G | N | SER- 414 | 2.92 | 168.06 | H-Bond (Protein Donor) |
| C4' | CB | LEU- 415 | 4.33 | 0 | Hydrophobic |
| O2B | N | LEU- 415 | 3.09 | 167.36 | H-Bond (Protein Donor) |
| C1' | CE2 | TYR- 416 | 4.02 | 0 | Hydrophobic |
| C2' | CD2 | TYR- 416 | 3.59 | 0 | Hydrophobic |
| C3' | CG | TYR- 416 | 4.32 | 0 | Hydrophobic |
| C4' | CD1 | TYR- 416 | 4.43 | 0 | Hydrophobic |
| O3' | N | TYR- 416 | 3 | 176 | H-Bond (Protein Donor) |
| O2G | CZ | ARG- 482 | 3.82 | 0 | Ionic (Protein Cationic) |
| O3G | CZ | ARG- 482 | 3.62 | 0 | Ionic (Protein Cationic) |
| O2G | NH1 | ARG- 482 | 3 | 170.36 | H-Bond (Protein Donor) |
| O3G | NH2 | ARG- 482 | 2.72 | 171.51 | H-Bond (Protein Donor) |
| O3G | NZ | LYS- 486 | 3.61 | 0 | Ionic (Protein Cationic) |
| O1A | NZ | LYS- 560 | 3.15 | 173.79 | H-Bond (Protein Donor) |
| O3A | NZ | LYS- 560 | 3.14 | 120.74 | H-Bond (Protein Donor) |
| O1A | NZ | LYS- 560 | 3.15 | 0 | Ionic (Protein Cationic) |
| O3G | NZ | LYS- 560 | 3.98 | 0 | Ionic (Protein Cationic) |
| C2' | CB | ASN- 564 | 4.29 | 0 | Hydrophobic |
| O1B | ND2 | ASN- 564 | 3.34 | 154.86 | H-Bond (Protein Donor) |
| C4' | CG2 | THR- 622 | 3.76 | 0 | Hydrophobic |
| C5' | CB | ASP- 623 | 4.31 | 0 | Hydrophobic |
| O2A | CA | CA- 904 | 2.61 | 0 | Metal Acceptor |
| O2B | CA | CA- 904 | 2.29 | 0 | Metal Acceptor |
| O1G | CA | CA- 904 | 2.26 | 0 | Metal Acceptor |
| O2A | CA | CA- 905 | 2.47 | 0 | Metal Acceptor |
