sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
2008-03-13
| Name: | Ribosomal protein L11 methyltransferase |
|---|---|
| ID: | PRMA_THET8 |
| AC: | Q84BQ9 |
| Organism: | Thermus thermophilus |
| Reign: | Bacteria |
| TaxID: | 300852 |
| EC Number: | 2.1.1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 92 % |
| B | 8 % |
| B-Factor: | 23.335 |
|---|---|
| Number of residues: | 41 |
| Including | |
| Standard Amino Acids: | 37 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.763 | 702.000 |
| % Hydrophobic | % Polar |
|---|---|
| 57.69 | 42.31 |
| According to VolSite | |
| HET Code: | SAH |
|---|---|
| Formula: | C14H20N6O5S |
| Molecular weight: | 384.411 g/mol |
| DrugBank ID: | DB01752 |
| Buried Surface Area: | 68.94 % |
| Polar Surface area: | 212.38 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 10 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| -14.5146 | -6.18438 | 35.3606 |
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 |
| SD | CG | LYS- 2 | 4.22 | 0 | Hydrophobic |
| C3' | CD | LYS- 2 | 3.98 | 0 | Hydrophobic |
| SD | CD1 | PHE- 99 | 3.42 | 0 | Hydrophobic |
| CG | CD1 | PHE- 99 | 3.83 | 0 | Hydrophobic |
| OXT | OG1 | THR- 107 | 2.56 | 152.43 | H-Bond (Protein Donor) |
| N | OD1 | ASP- 126 | 3.81 | 0 | Ionic (Ligand Cationic) |
| N | O | GLY- 128 | 2.81 | 152.57 | H-Bond (Ligand Donor) |
| O3' | OD2 | ASP- 149 | 3.48 | 132.49 | H-Bond (Ligand Donor) |
| O3' | OD1 | ASP- 149 | 2.6 | 170.74 | H-Bond (Ligand Donor) |
| O2' | OD2 | ASP- 149 | 2.64 | 167.02 | H-Bond (Ligand Donor) |
| N1 | OG | SER- 175 | 2.68 | 165.16 | H-Bond (Protein Donor) |
| CG | CB | ASN- 191 | 4.29 | 0 | Hydrophobic |
| O | ND2 | ASN- 191 | 2.9 | 166.11 | H-Bond (Protein Donor) |
| OXT | ND2 | ASN- 191 | 3.5 | 131.61 | H-Bond (Protein Donor) |
| C5' | CD2 | LEU- 192 | 4.33 | 0 | Hydrophobic |
| C1' | CD2 | LEU- 192 | 4.41 | 0 | Hydrophobic |
| N | O | HOH- 426 | 2.94 | 157.32 | H-Bond (Ligand Donor) |
