sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.950 Å
X-ray
2015-01-20
| Name: | CalS8 |
|---|---|
| ID: | Q8KNF6_MICEC |
| AC: | Q8KNF6 |
| Organism: | Micromonospora echinospora |
| Reign: | Bacteria |
| TaxID: | 1877 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 92 % |
| B | 8 % |
| B-Factor: | 34.093 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.475 | 594.000 |
| % Hydrophobic | % Polar |
|---|---|
| 43.18 | 56.82 |
| According to VolSite | |
| HET Code: | TMP |
|---|---|
| Formula: | C10H13N2O8P |
| Molecular weight: | 320.193 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 60.44 % |
| Polar Surface area: | 161.1 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 0 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 9.75814 | 17.7071 | -29.4341 |
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 |
| C5M | CG2 | ILE- 225 | 4.46 | 0 | Hydrophobic |
| O2P | NZ | LYS- 258 | 3.2 | 140.59 | H-Bond (Protein Donor) |
| O2P | NZ | LYS- 258 | 3.2 | 0 | Ionic (Protein Cationic) |
| C5M | CD | LYS- 258 | 4.25 | 0 | Hydrophobic |
| N3 | O | LEU- 267 | 2.7 | 163 | H-Bond (Ligand Donor) |
| O4 | N | LEU- 267 | 3.08 | 140.57 | H-Bond (Protein Donor) |
| C4' | CG1 | VAL- 272 | 3.95 | 0 | Hydrophobic |
| C1' | CG2 | VAL- 272 | 4.12 | 0 | Hydrophobic |
| O3' | N | GLY- 273 | 2.99 | 161.41 | H-Bond (Protein Donor) |
| C5' | CD1 | LEU- 277 | 3.54 | 0 | Hydrophobic |
| C5' | CE2 | PHE- 339 | 4.13 | 0 | Hydrophobic |
| C3' | CD2 | PHE- 339 | 3.79 | 0 | Hydrophobic |
| O3' | O | PHE- 339 | 2.71 | 149.68 | H-Bond (Ligand Donor) |
| O1P | NZ | LYS- 340 | 3.1 | 0 | Ionic (Protein Cationic) |
| O3P | NZ | LYS- 340 | 2.8 | 0 | Ionic (Protein Cationic) |
| O3P | NZ | LYS- 340 | 2.8 | 170.73 | H-Bond (Protein Donor) |
| C5' | CD | LYS- 340 | 4.45 | 0 | Hydrophobic |
| C3' | CG | LYS- 340 | 4.33 | 0 | Hydrophobic |
| O2 | O | HOH- 654 | 2.9 | 179.98 | H-Bond (Protein Donor) |
