sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.400 Å
X-ray
2013-08-12
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.220 | 6.220 | 6.220 | 0.000 | 6.220 | 1 |
| Name: | Beta-lactamase class B VIM-2 |
|---|---|
| ID: | Q9K2N0_PSEAI |
| AC: | Q9K2N0 |
| Organism: | Pseudomonas aeruginosa |
| Reign: | Bacteria |
| TaxID: | 287 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 95 % |
| B | 5 % |
| B-Factor: | 12.097 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 20 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | ZN ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.838 | 1390.500 |
| % Hydrophobic | % Polar |
|---|---|
| 42.72 | 57.28 |
| According to VolSite | |
| HET Code: | MCO |
|---|---|
| Formula: | C9H14NO3S |
| Molecular weight: | 216.277 g/mol |
| DrugBank ID: | DB02032 |
| Buried Surface Area: | 71.26 % |
| 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 |
|---|---|---|
| 75.9792 | 6.8885 | 58.116 |
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 |
| C7 | CD1 | PHE- 62 | 3.83 | 0 | Hydrophobic |
| C3 | CE2 | PHE- 62 | 4.07 | 0 | Hydrophobic |
| C6 | CD2 | TYR- 67 | 3.47 | 0 | Hydrophobic |
| C6 | CH2 | TRP- 87 | 4.17 | 0 | Hydrophobic |
| C3 | CZ2 | TRP- 87 | 3.73 | 0 | Hydrophobic |
| C1 | CB | HIS- 116 | 3.73 | 0 | Hydrophobic |
| S | SG | CYS- 198 | 3.94 | 0 | Hydrophobic |
| O3 | CZ | ARG- 205 | 3.7 | 0 | Ionic (Protein Cationic) |
| O3 | NH2 | ARG- 205 | 2.97 | 157.17 | H-Bond (Protein Donor) |
| O3 | N | ASN- 210 | 2.92 | 151.64 | H-Bond (Protein Donor) |
| O1 | ND2 | ASN- 210 | 2.98 | 147.51 | H-Bond (Protein Donor) |
