sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.600 Å
X-ray
1987-06-29
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 4.670 | 4.670 | 4.670 | 0.000 | 4.670 | 1 |
| 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 |
|---|---|
| E | 100 % |
| B-Factor: | 12.444 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 23 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.367 | 398.250 |
| % Hydrophobic | % Polar |
|---|---|
| 44.92 | 55.08 |
| According to VolSite | |
| HET Code: | 0FA |
|---|---|
| Formula: | C6H13N2O4P |
| Molecular weight: | 208.152 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 64.67 % |
| Polar Surface area: | 128.12 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 2 |
| Rings: | 0 |
| Aromatic rings: | 0 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 52.8282 | 18.2454 | -3.981 |
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 |
| N | O | ALA- 113 | 2.96 | 139.56 | H-Bond (Ligand Donor) |
| CD2 | CZ | PHE- 130 | 4.44 | 0 | Hydrophobic |
| CD2 | CD2 | LEU- 133 | 3.76 | 0 | Hydrophobic |
| CD1 | CG2 | VAL- 139 | 4.2 | 0 | Hydrophobic |
| CD2 | CG2 | VAL- 139 | 3.85 | 0 | Hydrophobic |
| CD1 | CB | HIS- 142 | 4.49 | 0 | Hydrophobic |
| N | OE2 | GLU- 143 | 3.36 | 128.49 | H-Bond (Ligand Donor) |
| CD1 | CG2 | ILE- 188 | 4.26 | 0 | Hydrophobic |
| CG | CD2 | LEU- 202 | 3.68 | 0 | Hydrophobic |
| O | NH2 | ARG- 203 | 2.82 | 148.47 | H-Bond (Protein Donor) |
| O | NH1 | ARG- 203 | 2.9 | 144.42 | H-Bond (Protein Donor) |
| O2 | NE2 | HIS- 231 | 2.79 | 165.99 | H-Bond (Protein Donor) |
| O1 | ZN | ZN- 321 | 2.79 | 0 | Metal Acceptor |
| O2 | ZN | ZN- 321 | 2.06 | 0 | Metal Acceptor |
