sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.550 Å
X-ray
2013-08-21
| Name: | tRNA (guanine-N(1)-)-methyltransferase |
|---|---|
| ID: | TRMD_HAEIN |
| AC: | P43912 |
| Organism: | Haemophilus influenzae |
| Reign: | Bacteria |
| TaxID: | 71421 |
| EC Number: | 2.1.1.228 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 21.459 |
|---|---|
| Number of residues: | 26 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.617 | 401.625 |
| % Hydrophobic | % Polar |
|---|---|
| 43.70 | 56.30 |
| According to VolSite | |
| HET Code: | 22L |
|---|---|
| Formula: | C12H8N2OS |
| Molecular weight: | 228.270 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 74.15 % |
| Polar Surface area: | 69.7 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 1 |
| X | Y | Z |
|---|---|---|
| 21.1059 | 65.0116 | 68.5203 |
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 |
| S9 | CB | LEU- 87 | 3.56 | 0 | Hydrophobic |
| N16 | N | ILE- 133 | 3.29 | 168.07 | H-Bond (Protein Donor) |
| N14 | O | TYR- 136 | 2.63 | 163.82 | H-Bond (Ligand Donor) |
| C5 | CB | LEU- 138 | 4.33 | 0 | Hydrophobic |
| O13 | N | LEU- 138 | 3.04 | 156.29 | H-Bond (Protein Donor) |
| S9 | CB | PRO- 144 | 3.49 | 0 | Hydrophobic |
