sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.700 Å
X-ray
2006-11-30
| Name: | Deoxyguanosine kinase |
|---|---|
| ID: | Q93IG4_MYCMI |
| AC: | Q93IG4 |
| Organism: | Mycoplasma mycoides subsp. mycoides SC |
| Reign: | Bacteria |
| TaxID: | 44101 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| D | 100 % |
| B-Factor: | 40.376 |
|---|---|
| Number of residues: | 44 |
| Including | |
| Standard Amino Acids: | 43 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.351 | 722.250 |
| % Hydrophobic | % Polar |
|---|---|
| 46.73 | 53.27 |
| According to VolSite | |
| HET Code: | DTP |
|---|---|
| Formula: | C10H12N5O12P3 |
| Molecular weight: | 487.150 g/mol |
| DrugBank ID: | DB03222 |
| Buried Surface Area: | 73.03 % |
| Polar Surface area: | 299.64 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 16 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| -90.5255 | 52.6001 | -12.7106 |
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 |
| C2' | CG2 | VAL- 9 | 3.41 | 0 | Hydrophobic |
| O2G | N | GLY- 10 | 3.09 | 146.37 | H-Bond (Protein Donor) |
| O3G | N | GLY- 12 | 2.79 | 142.98 | H-Bond (Protein Donor) |
| O3G | N | LYS- 13 | 2.84 | 170.16 | H-Bond (Protein Donor) |
| O3G | NZ | LYS- 13 | 3.19 | 169.6 | H-Bond (Protein Donor) |
| O1A | NZ | LYS- 13 | 3.14 | 169.95 | H-Bond (Protein Donor) |
| O3A | NZ | LYS- 13 | 3.24 | 126.31 | H-Bond (Protein Donor) |
| O3G | NZ | LYS- 13 | 3.19 | 0 | Ionic (Protein Cationic) |
| O1A | NZ | LYS- 13 | 3.14 | 0 | Ionic (Protein Cationic) |
| O1G | N | SER- 14 | 3.06 | 171.02 | H-Bond (Protein Donor) |
| O1G | OG | SER- 14 | 2.8 | 168.93 | H-Bond (Protein Donor) |
| C1' | CE1 | PHE- 39 | 4.24 | 0 | Hydrophobic |
| C4' | CE1 | PHE- 39 | 3.96 | 0 | Hydrophobic |
| O3' | OH | TYR- 43 | 2.6 | 134.67 | H-Bond (Protein Donor) |
| N6 | OE1 | GLN- 54 | 3.05 | 146.59 | H-Bond (Ligand Donor) |
| N1 | OE1 | GLN- 54 | 3.07 | 147.13 | H-Bond (Ligand Donor) |
| O2B | OD2 | ASP- 77 | 2.66 | 150.5 | H-Bond (Protein Donor) |
| O1A | CZ | ARG- 78 | 3.47 | 0 | Ionic (Protein Cationic) |
| N6 | OD1 | ASP- 83 | 2.66 | 150.17 | H-Bond (Ligand Donor) |
| DuAr | DuAr | PHE- 86 | 3.62 | 0 | Aromatic Face/Face |
| C2' | CE2 | PHE- 86 | 3.93 | 0 | Hydrophobic |
| O3' | OE2 | GLU- 150 | 2.71 | 164.3 | H-Bond (Ligand Donor) |
| O2G | MG | MG- 1202 | 2.14 | 0 | Metal Acceptor |
| O1B | MG | MG- 1202 | 2.26 | 0 | Metal Acceptor |
| O2A | MG | MG- 1202 | 2.18 | 0 | Metal Acceptor |
