sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.900 Å
X-ray
2006-08-24
| Name: | Guanylate kinase |
|---|---|
| ID: | KGUA_STAAC |
| AC: | Q5HGM3 |
| Organism: | Staphylococcus aureus |
| Reign: | Bacteria |
| TaxID: | 93062 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 21.731 |
|---|---|
| Number of residues: | 38 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | K |
| Ligandability | Volume (Å3) |
|---|---|
| 0.160 | 749.250 |
| % Hydrophobic | % Polar |
|---|---|
| 38.74 | 61.26 |
| According to VolSite | |
| HET Code: | 5GP |
|---|---|
| Formula: | C10H12N5O8P |
| Molecular weight: | 361.205 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 69.58 % |
| Polar Surface area: | 217.22 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 11 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 8.75108 | -25.0599 | 58.6061 |
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 |
| O1P | CZ | ARG- 43 | 3.83 | 0 | Ionic (Protein Cationic) |
| O2P | CZ | ARG- 43 | 3.79 | 0 | Ionic (Protein Cationic) |
| O1P | NH2 | ARG- 43 | 3.1 | 170.63 | H-Bond (Protein Donor) |
| O2P | NE | ARG- 43 | 2.79 | 149.72 | H-Bond (Protein Donor) |
| O1P | OH | TYR- 55 | 2.64 | 147.53 | H-Bond (Protein Donor) |
| N1 | OE1 | GLU- 74 | 2.61 | 145.7 | H-Bond (Ligand Donor) |
| N1 | OE2 | GLU- 74 | 3.29 | 136.41 | H-Bond (Ligand Donor) |
| N2 | OE2 | GLU- 74 | 2.8 | 162.79 | H-Bond (Ligand Donor) |
| C5' | CD2 | TYR- 78 | 3.63 | 0 | Hydrophobic |
| O2P | OH | TYR- 83 | 2.55 | 136.76 | H-Bond (Protein Donor) |
| C5' | CZ | TYR- 83 | 3.76 | 0 | Hydrophobic |
| C4' | CE1 | TYR- 83 | 4.49 | 0 | Hydrophobic |
| C1' | CD1 | TYR- 83 | 4.45 | 0 | Hydrophobic |
| O2' | OE2 | GLU- 103 | 2.73 | 160.6 | H-Bond (Ligand Donor) |
| C1' | CB | GLU- 105 | 4.25 | 0 | Hydrophobic |
| N2 | OE1 | GLU- 105 | 2.75 | 162.07 | H-Bond (Ligand Donor) |
| N3 | N | GLU- 105 | 3.12 | 166.2 | H-Bond (Protein Donor) |
