sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.800 Å
X-ray
2007-04-11
| Name: | Putative S-adenosyl-L-methionine-dependent methyltransferase ML2640 |
|---|---|
| ID: | Y2640_MYCLE |
| AC: | Q9CCZ4 |
| Organism: | Mycobacterium leprae |
| Reign: | Bacteria |
| TaxID: | 272631 |
| EC Number: | 2.1.1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 27.658 |
|---|---|
| Number of residues: | 23 |
| Including | |
| Standard Amino Acids: | 23 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.622 | 546.750 |
| % Hydrophobic | % Polar |
|---|---|
| 44.44 | 55.56 |
| According to VolSite | |
| HET Code: | SAM |
|---|---|
| Formula: | C15H23N6O5S |
| Molecular weight: | 399.445 g/mol |
| DrugBank ID: | DB00118 |
| Buried Surface Area: | 55.17 % |
| 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 |
|---|---|---|
| -5.94741 | -27.4134 | -2.06941 |
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 |
| C4' | CB | ALA- 110 | 4.08 | 0 | Hydrophobic |
| C1' | CB | ALA- 110 | 3.48 | 0 | Hydrophobic |
| O3' | OD2 | ASP- 132 | 2.67 | 130.89 | H-Bond (Ligand Donor) |
| O2' | OD1 | ASP- 132 | 2.85 | 163.51 | H-Bond (Ligand Donor) |
| N6 | OD1 | ASP- 161 | 2.79 | 142.08 | H-Bond (Ligand Donor) |
| N1 | N | LEU- 162 | 2.74 | 174.64 | H-Bond (Protein Donor) |
