sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.500 Å
X-ray
2002-01-08
| Name: | Metallo-beta-lactamase type 2 |
|---|---|
| ID: | BLAB_BACFG |
| AC: | P25910 |
| Organism: | Bacteroides fragilis |
| Reign: | Bacteria |
| TaxID: | 817 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 38.239 |
|---|---|
| Number of residues: | 24 |
| Including | |
| Standard Amino Acids: | 22 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | ZN ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 1.146 | 1360.125 |
| % Hydrophobic | % Polar |
|---|---|
| 38.71 | 61.29 |
| According to VolSite | |
| HET Code: | 113 |
|---|---|
| Formula: | C15H13O8 |
| Molecular weight: | 321.259 g/mol |
| DrugBank ID: | DB02593 |
| Buried Surface Area: | 44.46 % |
| Polar Surface area: | 125.35 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| -8.91174 | -28.6787 | 17.5869 |
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 |
| C2 | CB | TRP- 49 | 3.64 | 0 | Hydrophobic |
| C12 | CG1 | VAL- 52 | 4.24 | 0 | Hydrophobic |
| O30 | NZ | LYS- 184 | 3.97 | 0 | Ionic (Protein Cationic) |
| O16 | ND2 | ASN- 193 | 3.09 | 122.53 | H-Bond (Protein Donor) |
| O30 | N | ASN- 193 | 3.48 | 130.87 | H-Bond (Protein Donor) |
| C6 | CB | ASN- 193 | 3.67 | 0 | Hydrophobic |
| O19 | ZN | ZN- 302 | 2.63 | 0 | Metal Acceptor |
