sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.660 Å
X-ray
2011-08-01
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.260 | 8.260 | 8.260 | 0.000 | 8.260 | 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: | 8.432 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 29 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.122 | 340.875 |
| % Hydrophobic | % Polar |
|---|---|
| 39.60 | 60.40 |
| According to VolSite | |
| HET Code: | UBW |
|---|---|
| Formula: | C20H30N3O7P |
| Molecular weight: | 455.442 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 52.85 % |
| 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: | 14 |
| X | Y | Z |
|---|---|---|
| 11.3819 | 40.3724 | -6.34871 |
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 | 3.11 | 156.85 | H-Bond (Ligand Donor) |
| O20 | ND2 | ASN- 112 | 2.97 | 170.7 | H-Bond (Protein Donor) |
| C27 | CZ | PHE- 130 | 4.23 | 0 | Hydrophobic |
| C31 | CE2 | PHE- 130 | 3.69 | 0 | Hydrophobic |
| C27 | CD2 | LEU- 133 | 3.79 | 0 | Hydrophobic |
| C26 | CG2 | VAL- 139 | 4.1 | 0 | Hydrophobic |
| C27 | CG2 | VAL- 139 | 3.75 | 0 | Hydrophobic |
| C26 | CB | HIS- 142 | 4.36 | 0 | Hydrophobic |
| O22 | OE1 | GLU- 143 | 2.6 | 177.4 | H-Bond (Protein Donor) |
| N13 | OE2 | GLU- 143 | 3.3 | 140.68 | H-Bond (Ligand Donor) |
| C7 | CE2 | TYR- 157 | 4.08 | 0 | Hydrophobic |
| N10 | OH | TYR- 157 | 3.36 | 144.85 | H-Bond (Ligand Donor) |
| C26 | CG2 | ILE- 188 | 4.09 | 0 | Hydrophobic |
| C29 | CD2 | LEU- 202 | 3.89 | 0 | Hydrophobic |
| C31 | CD1 | LEU- 202 | 4.07 | 0 | Hydrophobic |
| C25 | CD2 | LEU- 202 | 3.65 | 0 | Hydrophobic |
| O28 | NH1 | ARG- 203 | 2.84 | 144.14 | H-Bond (Protein Donor) |
| O28 | NH2 | ARG- 203 | 2.92 | 139.74 | H-Bond (Protein Donor) |
| O23 | NE2 | HIS- 231 | 2.85 | 174.82 | H-Bond (Protein Donor) |
| O23 | ZN | ZN- 326 | 1.97 | 0 | Metal Acceptor |
