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
2011-12-23
| Name: | Ribosomal RNA large subunit methyltransferase K/L |
|---|---|
| ID: | RLMKL_ECOLI |
| AC: | P75864 |
| Organism: | Escherichia coli |
| Reign: | Bacteria |
| TaxID: | 83333 |
| EC Number: | 2.1.1.173 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 53.128 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.203 | 462.375 |
| % Hydrophobic | % Polar |
|---|---|
| 50.36 | 49.64 |
| According to VolSite | |
| HET Code: | SAM |
|---|---|
| Formula: | C15H23N6O5S |
| Molecular weight: | 399.445 g/mol |
| DrugBank ID: | DB00118 |
| Buried Surface Area: | 63.93 % |
| Polar Surface area: | 189.77 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 9 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 2 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| -13.578 | -31.7925 | 0.23512 |
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 |
| CB | CD2 | PHE- 523 | 4.44 | 0 | Hydrophobic |
| SD | CB | PHE- 546 | 4.46 | 0 | Hydrophobic |
| C4' | CB | PHE- 546 | 4.3 | 0 | Hydrophobic |
| C1' | CB | PHE- 546 | 4.15 | 0 | Hydrophobic |
| C4' | CB | TYR- 548 | 4.27 | 0 | Hydrophobic |
| C3' | CD1 | TYR- 548 | 4.29 | 0 | Hydrophobic |
| CG | CB | TYR- 548 | 3.3 | 0 | Hydrophobic |
| O3' | OD2 | ASP- 568 | 3.36 | 124.77 | H-Bond (Ligand Donor) |
| O3' | OD1 | ASP- 568 | 2.66 | 167.54 | H-Bond (Ligand Donor) |
| O2' | OD2 | ASP- 568 | 2.59 | 156.16 | H-Bond (Ligand Donor) |
| C2' | CE | MET- 569 | 4.06 | 0 | Hydrophobic |
| N3 | N | MET- 569 | 3.05 | 150.03 | H-Bond (Protein Donor) |
| C3' | CD2 | TYR- 573 | 4.48 | 0 | Hydrophobic |
| N6 | OD2 | ASP- 597 | 3.46 | 151.93 | H-Bond (Ligand Donor) |
| N1 | N | CYS- 598 | 2.95 | 159.67 | H-Bond (Protein Donor) |
| N | OD2 | ASP- 615 | 3.25 | 152.2 | H-Bond (Ligand Donor) |
| N | OD2 | ASP- 615 | 3.25 | 0 | Ionic (Ligand Cationic) |
| N7 | OG | SER- 620 | 3.12 | 155.06 | H-Bond (Protein Donor) |
| O | O | HOH- 902 | 3.16 | 174.6 | H-Bond (Protein Donor) |
