sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
1999-11-08
| Name: | Metallo-beta-lactamase type 2 |
|---|---|
| ID: | BLAB_SERMA |
| AC: | P52699 |
| Organism: | Serratia marcescens |
| Reign: | Bacteria |
| TaxID: | 615 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 41.618 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 4 |
| Cofactors: | |
| Metals: | ZN ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 1.033 | 587.250 |
| % Hydrophobic | % Polar |
|---|---|
| 58.05 | 41.95 |
| According to VolSite | |
| HET Code: | MCI |
|---|---|
| Formula: | C19H18N5O3S2 |
| Molecular weight: | 428.508 g/mol |
| DrugBank ID: | DB02706 |
| Buried Surface Area: | 58.01 % |
| Polar Surface area: | 180.2 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| 23.8943 | 16.6614 | 133.294 |
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 |
| C6 | CG | GLU- 23 | 3.2 | 0 | Hydrophobic |
| C4 | CB | GLU- 23 | 3.68 | 0 | Hydrophobic |
| C12 | CG1 | VAL- 25 | 3.4 | 0 | Hydrophobic |
| C37 | CD2 | TRP- 28 | 4.02 | 0 | Hydrophobic |
| DuAr | DuAr | TRP- 28 | 3.74 | 0 | Aromatic Face/Face |
| S36 | CG1 | VAL- 31 | 3.93 | 0 | Hydrophobic |
| C3 | CG1 | VAL- 31 | 3.85 | 0 | Hydrophobic |
| C4 | CB | LYS- 33 | 3.45 | 0 | Hydrophobic |
| C5 | CB | LYS- 33 | 4.01 | 0 | Hydrophobic |
| C6 | CD1 | PHE- 51 | 3.37 | 0 | Hydrophobic |
| C6 | CB | PHE- 51 | 3.75 | 0 | Hydrophobic |
| C19 | CB | HIS- 79 | 4.16 | 0 | Hydrophobic |
| C19 | CB | ASP- 81 | 4.49 | 0 | Hydrophobic |
| C1 | CB | ASP- 81 | 3.5 | 0 | Hydrophobic |
| C6 | CB | ASP- 81 | 3.53 | 0 | Hydrophobic |
| S20 | SG | CYS- 158 | 4.39 | 0 | Hydrophobic |
| O29 | NZ | LYS- 161 | 3.23 | 148.67 | H-Bond (Protein Donor) |
| O30 | NZ | LYS- 161 | 2.75 | 146.14 | H-Bond (Protein Donor) |
| O29 | NZ | LYS- 161 | 3.23 | 0 | Ionic (Protein Cationic) |
| O30 | NZ | LYS- 161 | 2.75 | 0 | Ionic (Protein Cationic) |
| O29 | N | ASN- 167 | 2.92 | 148.4 | H-Bond (Protein Donor) |
