sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
2006-05-12
| Name: | U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase |
|---|---|
| ID: | MET16_HUMAN |
| AC: | Q86W50 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 92 % |
| C | 8 % |
| B-Factor: | 46.231 |
|---|---|
| Number of residues: | 41 |
| Including | |
| Standard Amino Acids: | 39 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.935 | 499.500 |
| % Hydrophobic | % Polar |
|---|---|
| 52.70 | 47.30 |
| According to VolSite | |
| HET Code: | SAH |
|---|---|
| Formula: | C14H20N6O5S |
| Molecular weight: | 384.411 g/mol |
| DrugBank ID: | DB01752 |
| Buried Surface Area: | 72.89 % |
| 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 |
|---|---|---|
| 58.8083 | 23.7651 | 3.85638 |
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 | CD2 | LEU- 38 | 3.83 | 0 | Hydrophobic |
| CG | CD2 | LEU- 38 | 3.72 | 0 | Hydrophobic |
| O | CZ | ARG- 45 | 3.37 | 0 | Ionic (Protein Cationic) |
| OXT | CZ | ARG- 45 | 3.5 | 0 | Ionic (Protein Cationic) |
| O | NH2 | ARG- 45 | 3.28 | 125.65 | H-Bond (Protein Donor) |
| O | NE | ARG- 45 | 2.61 | 163.77 | H-Bond (Protein Donor) |
| OXT | NH2 | ARG- 45 | 2.91 | 144.65 | H-Bond (Protein Donor) |
| OXT | NE | ARG- 45 | 3.22 | 131.67 | H-Bond (Protein Donor) |
| N | O | GLY- 73 | 2.96 | 163.83 | H-Bond (Ligand Donor) |
| O3' | OE1 | GLU- 96 | 2.75 | 170.29 | H-Bond (Ligand Donor) |
| O3' | OE2 | GLU- 96 | 3.49 | 132.85 | H-Bond (Ligand Donor) |
| O2' | OE2 | GLU- 96 | 2.71 | 158.64 | H-Bond (Ligand Donor) |
| C1' | CG2 | VAL- 97 | 4.21 | 0 | Hydrophobic |
| N6 | O | THR- 127 | 2.9 | 171.98 | H-Bond (Ligand Donor) |
| CG | CB | ASN- 147 | 4.1 | 0 | Hydrophobic |
| O | ND2 | ASN- 147 | 3.21 | 155.87 | H-Bond (Protein Donor) |
| C5' | CG | PRO- 149 | 3.94 | 0 | Hydrophobic |
| C1' | CG | PRO- 149 | 4.24 | 0 | Hydrophobic |
| N | O | HOH- 402 | 2.98 | 160.27 | H-Bond (Ligand Donor) |
