sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
2015-08-09
| Name: | Uncharacterized protein MJ0489 |
|---|---|
| ID: | Y489_METJA |
| AC: | Q57913 |
| Organism: | Methanocaldococcus jannaschii |
| Reign: | Archaea |
| TaxID: | 243232 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 31.637 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.226 | 813.375 |
| % Hydrophobic | % Polar |
|---|---|
| 48.96 | 51.04 |
| According to VolSite | |
| HET Code: | SAM |
|---|---|
| Formula: | C15H23N6O5S |
| Molecular weight: | 399.445 g/mol |
| DrugBank ID: | DB00118 |
| Buried Surface Area: | 66.02 % |
| 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 |
|---|---|---|
| -3.89574 | 17.5483 | 35.5401 |
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 |
| O | NZ | LYS- 34 | 2.78 | 0 | Ionic (Protein Cationic) |
| CB | CD2 | TYR- 56 | 4.49 | 0 | Hydrophobic |
| SD | CD2 | TYR- 56 | 4.06 | 0 | Hydrophobic |
| C3' | CB | TYR- 56 | 3.99 | 0 | Hydrophobic |
| O3' | N | TYR- 56 | 3.4 | 144.87 | H-Bond (Protein Donor) |
| OXT | N | LEU- 57 | 3.23 | 157.87 | H-Bond (Protein Donor) |
| O3' | OD2 | ASP- 77 | 2.97 | 159.17 | H-Bond (Ligand Donor) |
| O2' | OD2 | ASP- 77 | 3.16 | 147.92 | H-Bond (Ligand Donor) |
| N3 | N | ILE- 78 | 3.25 | 137.23 | H-Bond (Protein Donor) |
| C2' | CG2 | ILE- 78 | 4.43 | 0 | Hydrophobic |
| N | O | LEU- 117 | 2.74 | 168.52 | H-Bond (Ligand Donor) |
| C1' | CG2 | THR- 118 | 4.48 | 0 | Hydrophobic |
| N | OE1 | GLU- 139 | 2.99 | 147.04 | H-Bond (Ligand Donor) |
| N | OE1 | GLU- 139 | 2.99 | 0 | Ionic (Ligand Cationic) |
| O | N | THR- 185 | 3.08 | 144.69 | H-Bond (Protein Donor) |
| O | OG1 | THR- 185 | 3.26 | 130.33 | H-Bond (Protein Donor) |
| OXT | N | THR- 185 | 3.39 | 155.11 | H-Bond (Protein Donor) |
| OXT | OG1 | THR- 185 | 2.64 | 170.26 | H-Bond (Protein Donor) |
| C3' | CZ | PHE- 221 | 3.94 | 0 | Hydrophobic |
| C2' | CE1 | PHE- 221 | 4.34 | 0 | Hydrophobic |
