sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.280 Å
X-ray
2011-08-01
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.310 | 8.310 | 8.310 | 0.000 | 8.310 | 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 |
|---|---|
| A | 100 % |
| B-Factor: | 7.352 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.244 | 374.625 |
| % Hydrophobic | % Polar |
|---|---|
| 41.44 | 58.56 |
| According to VolSite | |
| HET Code: | UBZ |
|---|---|
| Formula: | C19H28N3O7P |
| Molecular weight: | 441.415 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 52.68 % |
| Polar Surface area: | 169.52 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 3 |
| Rings: | 1 |
| Aromatic rings: | 1 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 13 |
| X | Y | Z |
|---|---|---|
| 11.5205 | 40.2798 | -6.4745 |
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 |
| N16 | OD1 | ASN- 112 | 3.04 | 156.63 | H-Bond (Ligand Donor) |
| O19 | ND2 | ASN- 112 | 2.97 | 168.23 | H-Bond (Protein Donor) |
| C5 | CB | PHE- 114 | 4.41 | 0 | Hydrophobic |
| C22 | CE1 | PHE- 130 | 4.18 | 0 | Hydrophobic |
| C26 | CE2 | PHE- 130 | 4.46 | 0 | Hydrophobic |
| C22 | CD2 | LEU- 133 | 3.89 | 0 | Hydrophobic |
| C22 | CG2 | VAL- 139 | 3.74 | 0 | Hydrophobic |
| C23 | CG2 | VAL- 139 | 4.13 | 0 | Hydrophobic |
| C23 | CB | HIS- 142 | 4.31 | 0 | Hydrophobic |
| O22 | OE1 | GLU- 143 | 2.61 | 178.99 | H-Bond (Protein Donor) |
| N13 | OE2 | GLU- 143 | 3.34 | 141.91 | H-Bond (Ligand Donor) |
| C7 | CE2 | TYR- 157 | 4.1 | 0 | Hydrophobic |
| N10 | OH | TYR- 157 | 3.3 | 158.15 | H-Bond (Ligand Donor) |
| C23 | CG2 | ILE- 188 | 4.12 | 0 | Hydrophobic |
| C25 | CD2 | LEU- 202 | 3.97 | 0 | Hydrophobic |
| C21 | CD2 | LEU- 202 | 3.65 | 0 | Hydrophobic |
| O24 | NH1 | ARG- 203 | 2.84 | 147.09 | H-Bond (Protein Donor) |
| O24 | NH2 | ARG- 203 | 2.95 | 141.42 | H-Bond (Protein Donor) |
| O23 | NE2 | HIS- 231 | 2.85 | 174.1 | H-Bond (Protein Donor) |
| O23 | ZN | ZN- 326 | 1.98 | 0 | Metal Acceptor |
