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
2011-07-29
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.720 | 7.720 | 7.720 | 0.000 | 7.720 | 2 |
| 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: | 6.715 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.328 | 405.000 |
| % Hydrophobic | % Polar |
|---|---|
| 43.33 | 56.67 |
| According to VolSite | |
| HET Code: | UBY |
|---|---|
| Formula: | C18H26N3O7P |
| Molecular weight: | 427.389 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 50.1 % |
| 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 |
|---|---|---|
| 11.6242 | -40.1367 | 6.56966 |
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 | 2.99 | 155.77 | H-Bond (Ligand Donor) |
| O19 | ND2 | ASN- 112 | 2.93 | 174 | H-Bond (Protein Donor) |
| C3 | CB | PHE- 114 | 4.41 | 0 | Hydrophobic |
| C23 | CE1 | PHE- 130 | 4.12 | 0 | Hydrophobic |
| C23 | CD2 | LEU- 133 | 3.9 | 0 | Hydrophobic |
| C21 | CG1 | VAL- 139 | 4.48 | 0 | Hydrophobic |
| C22 | CG2 | VAL- 139 | 4.13 | 0 | Hydrophobic |
| C23 | CG2 | VAL- 139 | 3.71 | 0 | Hydrophobic |
| C22 | CB | HIS- 142 | 4.28 | 0 | Hydrophobic |
| O22 | OE1 | GLU- 143 | 2.62 | 179.16 | H-Bond (Protein Donor) |
| N13 | OE2 | GLU- 143 | 3.29 | 144.73 | H-Bond (Ligand Donor) |
| C7 | CE2 | TYR- 157 | 4.1 | 0 | Hydrophobic |
| N10 | OH | TYR- 157 | 3.34 | 153.69 | H-Bond (Ligand Donor) |
| C22 | CG2 | ILE- 188 | 4.06 | 0 | Hydrophobic |
| C25 | CD2 | LEU- 202 | 4.15 | 0 | Hydrophobic |
| C21 | CD2 | LEU- 202 | 3.71 | 0 | Hydrophobic |
| O24 | NH1 | ARG- 203 | 2.84 | 145.79 | H-Bond (Protein Donor) |
| O24 | NH2 | ARG- 203 | 2.93 | 141.05 | H-Bond (Protein Donor) |
| O23 | NE2 | HIS- 231 | 2.84 | 173.75 | H-Bond (Protein Donor) |
| O23 | ZN | ZN- 410 | 1.98 | 0 | Metal Acceptor |
