sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.680 Å
X-ray
2008-10-29
| Name: | Thermolysin |
|---|---|
| ID: | THER_BACTH |
| AC: | P00800 |
| Organism: | Bacillus thermoproteolyticus |
| Reign: | Bacteria |
| TaxID: | 1427 |
| EC Number: | 3.4.24.27 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 20.014 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 23 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.538 | 286.875 |
| % Hydrophobic | % Polar |
|---|---|
| 50.59 | 49.41 |
| According to VolSite | |
| HET Code: | S7B |
|---|---|
| Formula: | C12H11O4 |
| Molecular weight: | 219.213 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 66.49 % |
| Polar Surface area: | 66.43 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 0 |
| Rings: | 2 |
| Aromatic rings: | 1 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| -9.88969 | 38.9841 | 3.56706 |
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 |
| C14 | CB | ASN- 112 | 3.39 | 0 | Hydrophobic |
| C13 | CZ | PHE- 130 | 4.14 | 0 | Hydrophobic |
| C13 | CD2 | LEU- 133 | 3.65 | 0 | Hydrophobic |
| C10 | CG2 | VAL- 139 | 3.44 | 0 | Hydrophobic |
| C9 | CG1 | VAL- 139 | 3.29 | 0 | Hydrophobic |
| C9 | CB | HIS- 142 | 4.1 | 0 | Hydrophobic |
| O6 | OE2 | GLU- 143 | 3.23 | 120.18 | H-Bond (Protein Donor) |
| O3 | OE2 | GLU- 143 | 2.64 | 143 | H-Bond (Protein Donor) |
| C10 | CG2 | ILE- 188 | 4 | 0 | Hydrophobic |
| C13 | CD2 | LEU- 202 | 4.14 | 0 | Hydrophobic |
| C10 | CD2 | LEU- 202 | 3.82 | 0 | Hydrophobic |
| O11 | NH2 | ARG- 203 | 2.91 | 170.96 | H-Bond (Protein Donor) |
| O4 | NE2 | HIS- 231 | 2.82 | 173.55 | H-Bond (Protein Donor) |
| O4 | ZN | ZN- 321 | 1.99 | 0 | Metal Acceptor |
| O3 | ZN | ZN- 321 | 2.66 | 0 | Metal Acceptor |
