sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.260 Å
X-ray
2012-01-19
| Name: | Beta-lactamase |
|---|---|
| ID: | Q9L5C8_ECOLX |
| AC: | Q9L5C8 |
| Organism: | Escherichia coli |
| Reign: | Bacteria |
| TaxID: | 562 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 5.882 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 4 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.087 | 317.250 |
| % Hydrophobic | % Polar |
|---|---|
| 26.60 | 73.40 |
| According to VolSite | |
| HET Code: | 0J6 |
|---|---|
| Formula: | C15H10N7O |
| Molecular weight: | 304.286 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 60.29 % |
| Polar Surface area: | 110.54 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| -7.51817 | 55.441 | 12.204 |
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 |
| O14 | ND2 | ASN- 104 | 2.83 | 165.42 | H-Bond (Protein Donor) |
| C10 | CB | TYR- 105 | 3.7 | 0 | Hydrophobic |
| C11 | CB | SER- 130 | 3.86 | 0 | Hydrophobic |
| O14 | ND2 | ASN- 132 | 2.94 | 139.33 | H-Bond (Protein Donor) |
| N4 | OG1 | THR- 235 | 3.5 | 149.89 | H-Bond (Protein Donor) |
| N5 | OG1 | THR- 235 | 2.71 | 177.93 | H-Bond (Protein Donor) |
| N3 | OG | SER- 237 | 2.7 | 159.42 | H-Bond (Protein Donor) |
