sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.020 Å
X-ray
2015-08-12
| Name: | Metallo-beta-lactamase |
|---|---|
| ID: | G5ELM3_SERMA |
| AC: | G5ELM3 |
| Organism: | Serratia marcescens |
| Reign: | Bacteria |
| TaxID: | 615 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 42.377 |
|---|---|
| Number of residues: | 20 |
| Including | |
| Standard Amino Acids: | 16 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | ZN ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.244 | 357.750 |
| % Hydrophobic | % Polar |
|---|---|
| 50.00 | 50.00 |
| According to VolSite | |
| HET Code: | X8Z |
|---|---|
| Formula: | C9H14NO3S |
| Molecular weight: | 216.277 g/mol |
| DrugBank ID: | DB01197 |
| Buried Surface Area: | 51.52 % |
| Polar Surface area: | 99.24 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 1 |
| Rings: | 1 |
| Aromatic rings: | 0 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| -30.2535 | 9.58536 | 1.35529 |
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 | CB | SER- 175 | 4.16 | 0 | Hydrophobic |
| O1 | OG1 | THR- 177 | 2.83 | 160.79 | H-Bond (Protein Donor) |
| C3 | CG2 | VAL- 179 | 3.83 | 0 | Hydrophobic |
| O3 | NH2 | ARG- 252 | 3 | 156.78 | H-Bond (Protein Donor) |
| O3 | NH1 | ARG- 252 | 3.48 | 134.51 | H-Bond (Protein Donor) |
| O3 | CZ | ARG- 252 | 3.68 | 0 | Ionic (Protein Cationic) |
