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
2012-06-06
| Name: | Spore photoproduct lyase |
|---|---|
| ID: | A4IQU1_GEOTN |
| AC: | A4IQU1 |
| Organism: | Geobacillus thermodenitrificans |
| Reign: | Bacteria |
| TaxID: | 420246 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 28.697 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 24 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.907 | 749.250 |
| % Hydrophobic | % Polar |
|---|---|
| 44.59 | 55.41 |
| According to VolSite | |
| HET Code: | 0TT |
|---|---|
| Formula: | C20H28N4O10 |
| Molecular weight: | 484.457 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 57.52 % |
| Polar Surface area: | 198.19 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 10 |
| H-Bond Donors: | 6 |
| Rings: | 4 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -20.8778 | -1.22597 | 23.7353 |
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 |
| N2 | O | LYS- 77 | 2.75 | 172.04 | H-Bond (Ligand Donor) |
| CH | CB | SER- 79 | 4.24 | 0 | Hydrophobic |
| O4 | N | SER- 79 | 3.08 | 152.55 | H-Bond (Protein Donor) |
| C8 | CD1 | TYR- 98 | 3.38 | 0 | Hydrophobic |
| CA | CE1 | TYR- 98 | 3.93 | 0 | Hydrophobic |
| CA | CG2 | THR- 102 | 4.08 | 0 | Hydrophobic |
| CH | CG | GLU- 137 | 4.16 | 0 | Hydrophobic |
| CH | SG | CYS- 140 | 4.5 | 0 | Hydrophobic |
| CM | SG | CYS- 140 | 3.2 | 0 | Hydrophobic |
| CM | CG2 | THR- 141 | 4.5 | 0 | Hydrophobic |
| C1 | CG1 | VAL- 172 | 3.71 | 0 | Hydrophobic |
| C3 | CG2 | ILE- 270 | 3.83 | 0 | Hydrophobic |
| C4 | CD | ARG- 273 | 3.72 | 0 | Hydrophobic |
| N4 | OH | TYR- 339 | 2.76 | 165.23 | H-Bond (Ligand Donor) |
