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
2005-12-02
| Name: | Lmo1582 protein |
|---|---|
| ID: | Q8Y6U9_LISMO |
| AC: | Q8Y6U9 |
| Organism: | Listeria monocytogenes serovar 1/2a |
| Reign: | Bacteria |
| TaxID: | 169963 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 43.378 |
|---|---|
| Number of residues: | 46 |
| Including | |
| Standard Amino Acids: | 41 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 5 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.658 | 408.375 |
| % Hydrophobic | % Polar |
|---|---|
| 48.76 | 51.24 |
| According to VolSite | |
| HET Code: | SAM |
|---|---|
| Formula: | C15H23N6O5S |
| Molecular weight: | 399.445 g/mol |
| DrugBank ID: | DB00118 |
| Buried Surface Area: | 75.72 % |
| 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 |
|---|---|---|
| 37.0226 | 22.412 | 47.4729 |
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 |
| N | OG1 | THR- 98 | 2.85 | 154.5 | H-Bond (Ligand Donor) |
| O | N | THR- 98 | 3.24 | 168.78 | H-Bond (Protein Donor) |
| C4' | CB | ALA- 126 | 4.1 | 0 | Hydrophobic |
| C1' | CB | ALA- 126 | 4.11 | 0 | Hydrophobic |
| OXT | N | THR- 129 | 3.01 | 134.22 | H-Bond (Protein Donor) |
| OXT | OG1 | THR- 129 | 2.5 | 166.46 | H-Bond (Protein Donor) |
| O | N | LEU- 132 | 3.11 | 152.5 | H-Bond (Protein Donor) |
| O3' | OD2 | ASP- 154 | 2.73 | 168.27 | H-Bond (Ligand Donor) |
| O2' | OD2 | ASP- 154 | 3.33 | 147.46 | H-Bond (Ligand Donor) |
| O2' | OD1 | ASP- 154 | 2.58 | 149.68 | H-Bond (Ligand Donor) |
| N3 | N | VAL- 155 | 3.41 | 151.2 | H-Bond (Protein Donor) |
| C3' | CD1 | LEU- 159 | 4.21 | 0 | Hydrophobic |
| N6 | OD1 | ASP- 180 | 2.9 | 172.39 | H-Bond (Ligand Donor) |
| N1 | N | GLY- 181 | 2.86 | 156.15 | H-Bond (Protein Donor) |
| CE | CB | ASP- 196 | 4.35 | 0 | Hydrophobic |
| CG | CB | ASP- 196 | 4.21 | 0 | Hydrophobic |
| C5' | CB | PRO- 198 | 4.39 | 0 | Hydrophobic |
| C1' | CG | PRO- 198 | 4.39 | 0 | Hydrophobic |
| N | O | HOH- 406 | 3.38 | 125.68 | H-Bond (Ligand Donor) |
| N | O | HOH- 414 | 2.73 | 174.74 | H-Bond (Ligand Donor) |
