sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.600 Å
X-ray
2007-10-31
| Name: | 16S rRNA methylase |
|---|---|
| ID: | Q763K9_ECOLX |
| AC: | Q763K9 |
| Organism: | Escherichia coli |
| Reign: | Bacteria |
| TaxID: | 562 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 32.488 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.823 | 688.500 |
| % Hydrophobic | % Polar |
|---|---|
| 42.16 | 57.84 |
| According to VolSite | |
| HET Code: | 5GP |
|---|---|
| Formula: | C10H12N5O8P |
| Molecular weight: | 361.205 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 64.98 % |
| 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 |
|---|---|---|
| 13.4176 | 23.3478 | 25.9272 |
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 | OG | SER- 83 | 2.7 | 154.22 | H-Bond (Protein Donor) |
| O2P | OG | SER- 83 | 3.16 | 130.31 | H-Bond (Protein Donor) |
| C4' | CB | ALA- 111 | 3.93 | 0 | Hydrophobic |
| C1' | CB | ALA- 111 | 3.89 | 0 | Hydrophobic |
| O3' | OD2 | ASP- 131 | 3.15 | 148.56 | H-Bond (Ligand Donor) |
| O2' | OD1 | ASP- 131 | 3.25 | 151.49 | H-Bond (Ligand Donor) |
| C1' | CG1 | ILE- 132 | 4.18 | 0 | Hydrophobic |
| N1 | N | VAL- 158 | 2.97 | 151.33 | H-Bond (Protein Donor) |
| C5' | CD1 | LEU- 178 | 3.9 | 0 | Hydrophobic |
