sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.800 Å
X-ray
2012-05-01
| Name: | Metallo-beta-lactamase type 2 |
|---|---|
| ID: | BLAN1_KLEPN |
| AC: | C7C422 |
| Organism: | Klebsiella pneumoniae |
| Reign: | Bacteria |
| TaxID: | 573 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 85 % |
| B | 15 % |
| B-Factor: | 10.176 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | ZN ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 1.239 | 1383.750 |
| % Hydrophobic | % Polar |
|---|---|
| 50.00 | 50.00 |
| According to VolSite | |
| HET Code: | PNK |
|---|---|
| Formula: | C16H19N2O5S |
| Molecular weight: | 351.397 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 71.36 % |
| Polar Surface area: | 151.27 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 1 |
| Anionic atoms: | 2 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -2.40625 | 9.54567 | 26.9655 |
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 |
| C12 | CG2 | THR- 34 | 3.61 | 0 | Hydrophobic |
| C3 | CD2 | LEU- 65 | 3.66 | 0 | Hydrophobic |
| C8 | CG | LEU- 65 | 4.07 | 0 | Hydrophobic |
| C10 | CD2 | LEU- 65 | 3.72 | 0 | Hydrophobic |
| C8 | CE | MET- 67 | 3.46 | 0 | Hydrophobic |
| N2 | O | GLY- 69 | 2.91 | 175.76 | H-Bond (Ligand Donor) |
| C10 | CB | PHE- 70 | 4.44 | 0 | Hydrophobic |
| C13 | CE2 | PHE- 70 | 4.5 | 0 | Hydrophobic |
| C12 | CD2 | PHE- 70 | 3.86 | 0 | Hydrophobic |
| C13 | CG1 | VAL- 73 | 4.31 | 0 | Hydrophobic |
| C4 | CH2 | TRP- 93 | 4.47 | 0 | Hydrophobic |
| C15 | CZ3 | TRP- 93 | 4.32 | 0 | Hydrophobic |
| C15 | CB | GLN- 123 | 4.18 | 0 | Hydrophobic |
| O5 | N | ASP- 124 | 3.07 | 143.27 | H-Bond (Protein Donor) |
| O1 | NZ | LYS- 211 | 2.78 | 142.43 | H-Bond (Protein Donor) |
| O2 | NZ | LYS- 211 | 3.2 | 154.61 | H-Bond (Protein Donor) |
| O1 | NZ | LYS- 211 | 2.78 | 0 | Ionic (Protein Cationic) |
| O2 | NZ | LYS- 211 | 3.2 | 0 | Ionic (Protein Cationic) |
| O1 | N | ASN- 220 | 2.99 | 146.82 | H-Bond (Protein Donor) |
| S1 | CB | ASN- 220 | 4.49 | 0 | Hydrophobic |
| C12 | CB | ASN- 220 | 3.76 | 0 | Hydrophobic |
| O4 | ZN | ZN- 302 | 2.45 | 0 | Metal Acceptor |
| O2 | ZN | ZN- 303 | 2.19 | 0 | Metal Acceptor |
