sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.750 Å
X-ray
2012-06-26
| Name: | Arsenic methyltransferase |
|---|---|
| ID: | C0JV69_9RHOD |
| AC: | C0JV69 |
| Organism: | Cyanidioschyzon sp. 5508 |
| Reign: | Eukaryota |
| TaxID: | 610260 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 50.737 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.822 | 482.625 |
| % Hydrophobic | % Polar |
|---|---|
| 51.05 | 48.95 |
| According to VolSite | |
| HET Code: | SAM |
|---|---|
| Formula: | C15H23N6O5S |
| Molecular weight: | 399.445 g/mol |
| DrugBank ID: | DB00118 |
| Buried Surface Area: | 68.21 % |
| 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 |
|---|---|---|
| -6.86181 | 26.7177 | 28.9512 |
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 |
| CG | CB | TYR- 70 | 4.11 | 0 | Hydrophobic |
| SD | CB | TYR- 70 | 4.35 | 0 | Hydrophobic |
| N | O | GLY- 91 | 2.75 | 157.82 | H-Bond (Ligand Donor) |
| O3' | OD1 | ASP- 115 | 2.58 | 141.74 | H-Bond (Ligand Donor) |
| O3' | OD2 | ASP- 115 | 3.4 | 146.82 | H-Bond (Ligand Donor) |
| O2' | OD1 | ASP- 115 | 3.47 | 133.65 | H-Bond (Ligand Donor) |
| O2' | OD2 | ASP- 115 | 2.52 | 143.23 | H-Bond (Ligand Donor) |
| C2' | CE | MET- 116 | 4.47 | 0 | Hydrophobic |
| N3 | N | MET- 116 | 3.48 | 121.3 | H-Bond (Protein Donor) |
| C2' | CD1 | LEU- 117 | 3.9 | 0 | Hydrophobic |
| O3' | NE2 | GLN- 120 | 3.29 | 172.46 | H-Bond (Protein Donor) |
| N1 | N | ILE- 151 | 2.96 | 156.11 | H-Bond (Protein Donor) |
| N6 | OE1 | GLU- 152 | 3.03 | 136.15 | H-Bond (Ligand Donor) |
| CE | CB | CYS- 174 | 4.22 | 0 | Hydrophobic |
| C5' | CD1 | LEU- 178 | 3.85 | 0 | Hydrophobic |
