sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.500 Å
X-ray
2013-10-29
| Name: | Putative SAM-dependent methyltransferase |
|---|---|
| ID: | Q0X0A7_STRLS |
| AC: | Q0X0A7 |
| Organism: | Streptomyces lasaliensis |
| Reign: | Bacteria |
| TaxID: | 324833 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 14.507 |
|---|---|
| Number of residues: | 38 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.277 | 769.500 |
| % Hydrophobic | % Polar |
|---|---|
| 53.95 | 46.05 |
| According to VolSite | |
| HET Code: | SAH |
|---|---|
| Formula: | C14H20N6O5S |
| Molecular weight: | 384.411 g/mol |
| DrugBank ID: | DB01752 |
| Buried Surface Area: | 66.92 % |
| 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 |
|---|---|---|
| -2.31077 | 102.299 | 38.0721 |
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 |
| C5' | CE1 | PHE- 5 | 4.07 | 0 | Hydrophobic |
| C2' | CD1 | PHE- 5 | 3.44 | 0 | Hydrophobic |
| C3' | CE2 | TYR- 9 | 4.01 | 0 | Hydrophobic |
| O3' | OH | TYR- 9 | 2.51 | 153.39 | H-Bond (Protein Donor) |
| SD | CE2 | TRP- 21 | 3.69 | 0 | Hydrophobic |
| N | O | GLY- 47 | 2.78 | 160.92 | H-Bond (Ligand Donor) |
| O3' | OD1 | ASP- 68 | 3.24 | 123.77 | H-Bond (Ligand Donor) |
| O3' | OD2 | ASP- 68 | 2.6 | 166.71 | H-Bond (Ligand Donor) |
| O2' | OD1 | ASP- 68 | 2.65 | 162.58 | H-Bond (Ligand Donor) |
| N3 | N | LEU- 69 | 3.19 | 138.05 | H-Bond (Protein Donor) |
| N6 | OD1 | ASP- 94 | 2.84 | 155.83 | H-Bond (Ligand Donor) |
| N1 | N | ALA- 95 | 2.84 | 178.54 | H-Bond (Protein Donor) |
| N | O | SER- 111 | 2.84 | 170.43 | H-Bond (Ligand Donor) |
| C1' | CD1 | LEU- 113 | 4.15 | 0 | Hydrophobic |
| N | O | HOH- 574 | 2.78 | 159.8 | H-Bond (Ligand Donor) |
| OXT | O | HOH- 576 | 2.84 | 179.97 | H-Bond (Protein Donor) |
