sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.200 Å
X-ray
2006-11-10
| Name: | S-adenosyl-L-methionine-binding protein AF_0241 |
|---|---|
| ID: | Y241_ARCFU |
| AC: | O29998 |
| Organism: | Archaeoglobus fulgidus |
| Reign: | Archaea |
| TaxID: | 224325 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 17 % |
| B | 83 % |
| B-Factor: | 24.665 |
|---|---|
| Number of residues: | 37 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.226 | 438.750 |
| % Hydrophobic | % Polar |
|---|---|
| 56.15 | 43.85 |
| According to VolSite | |
| HET Code: | SAM |
|---|---|
| Formula: | C15H23N6O5S |
| Molecular weight: | 399.445 g/mol |
| DrugBank ID: | DB00118 |
| Buried Surface Area: | 79.84 % |
| 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 |
|---|---|---|
| 11.6466 | 22.8396 | 13.0599 |
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 |
| C1' | CG | GLN- 16 | 4.24 | 0 | Hydrophobic |
| C2' | CB | ALA- 19 | 3.61 | 0 | Hydrophobic |
| SD | SD | MET- 57 | 4.06 | 0 | Hydrophobic |
| N6 | OD1 | ASP- 58 | 2.92 | 173.25 | H-Bond (Ligand Donor) |
| N1 | N | LYS- 59 | 3.15 | 160.3 | H-Bond (Protein Donor) |
| OXT | NE | ARG- 82 | 2.61 | 131.07 | H-Bond (Protein Donor) |
| OXT | CZ | ARG- 82 | 2.9 | 0 | Ionic (Protein Cationic) |
| C4' | CG | PRO- 84 | 4.09 | 0 | Hydrophobic |
| C1' | CG | PRO- 84 | 4.1 | 0 | Hydrophobic |
| SD | CG | PRO- 84 | 4.11 | 0 | Hydrophobic |
| O | N | LEU- 92 | 2.83 | 157.01 | H-Bond (Protein Donor) |
| N | OD2 | ASP- 111 | 3.52 | 0 | Ionic (Ligand Cationic) |
| C5' | CB | ASP- 111 | 4.22 | 0 | Hydrophobic |
| C2' | CD2 | LEU- 113 | 4.38 | 0 | Hydrophobic |
| N7 | N | LEU- 113 | 3.11 | 158.01 | H-Bond (Protein Donor) |
| N6 | OG | SER- 116 | 2.8 | 137.72 | H-Bond (Ligand Donor) |
| O | NZ | LYS- 122 | 3.5 | 0 | Ionic (Protein Cationic) |
| O2' | O | HOH- 207 | 2.92 | 155.22 | H-Bond (Ligand Donor) |
