sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.410 Å
X-ray
2009-01-16
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 5.230 | 5.230 | 5.230 | 0.000 | 5.230 | 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: | 10.973 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.127 | 324.000 |
| % Hydrophobic | % Polar |
|---|---|
| 36.46 | 63.54 |
| According to VolSite | |
| HET Code: | UB2 |
|---|---|
| Formula: | C18H26N3O7P |
| Molecular weight: | 427.389 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 47.09 % |
| 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: | 12 |
| X | Y | Z |
|---|---|---|
| -11.2489 | 40.646 | 6.66134 |
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 |
| N17 | OD1 | ASN- 112 | 3.11 | 151.71 | H-Bond (Ligand Donor) |
| C25 | CB | ASN- 112 | 4.11 | 0 | Hydrophobic |
| O21 | ND2 | ASN- 112 | 2.96 | 173.67 | H-Bond (Protein Donor) |
| N13 | O | ALA- 113 | 2.89 | 120.8 | H-Bond (Ligand Donor) |
| C28 | CB | PHE- 114 | 4.38 | 0 | Hydrophobic |
| C29 | CB | ASN- 116 | 4.45 | 0 | Hydrophobic |
| C25 | CZ | PHE- 130 | 3.9 | 0 | Hydrophobic |
| C24 | CE2 | PHE- 130 | 3.95 | 0 | Hydrophobic |
| C15 | CG1 | VAL- 139 | 4.32 | 0 | Hydrophobic |
| O12 | OE1 | GLU- 143 | 2.73 | 158.65 | H-Bond (Protein Donor) |
| N13 | OE2 | GLU- 143 | 3.24 | 141.73 | H-Bond (Ligand Donor) |
| C5 | CE2 | TYR- 157 | 4.1 | 0 | Hydrophobic |
| C22 | CD2 | LEU- 202 | 4.35 | 0 | Hydrophobic |
| C25 | CD2 | LEU- 202 | 4.1 | 0 | Hydrophobic |
| O26 | NH2 | ARG- 203 | 2.92 | 140.38 | H-Bond (Protein Donor) |
| O26 | NH1 | ARG- 203 | 2.81 | 146.06 | H-Bond (Protein Donor) |
| O11 | NE2 | HIS- 231 | 2.85 | 175.9 | H-Bond (Protein Donor) |
| O11 | ZN | ZN- 321 | 1.97 | 0 | Metal Acceptor |
