sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.930 Å
X-ray
2001-08-19
| Name: | Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase |
|---|---|
| ID: | MCE_VACCW |
| AC: | P07617 |
| Organism: | Vaccinia virus ) |
| Reign: | Viruses |
| TaxID: | 10254 |
| EC Number: | 2.1.1.57 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 18.894 |
|---|---|
| Number of residues: | 19 |
| Including | |
| Standard Amino Acids: | 18 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.496 | 253.125 |
| % Hydrophobic | % Polar |
|---|---|
| 56.00 | 44.00 |
| According to VolSite | |
| HET Code: | NDM |
|---|---|
| Formula: | C7H14N5O |
| Molecular weight: | 184.219 g/mol |
| DrugBank ID: | DB01978 |
| Buried Surface Area: | 42.97 % |
| Polar Surface area: | 79.12 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 4 |
| Rings: | 2 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 0 |
| X | Y | Z |
|---|---|---|
| 17.4163 | 13.2124 | 20.866 |
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 |
| CN9 | CE2 | PHE- 180 | 4.45 | 0 | Hydrophobic |
| DuAr | DuAr | PHE- 180 | 3.8 | 0 | Aromatic Face/Face |
| N2 | OD2 | ASP- 182 | 3.28 | 145.72 | H-Bond (Ligand Donor) |
| N2 | OE1 | GLU- 233 | 3.21 | 131.52 | H-Bond (Ligand Donor) |
| N1 | OE1 | GLU- 233 | 2.67 | 159.51 | H-Bond (Ligand Donor) |
