sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.100 Å
X-ray
2007-06-18
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.680 | 6.680 | 6.680 | 0.000 | 6.680 | 1 |
| Name: | Tyrosine-protein phosphatase non-receptor type 1 |
|---|---|
| ID: | PTN1_HUMAN |
| AC: | P18031 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 3.1.3.48 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 25.428 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 29 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.644 | 459.000 |
| % Hydrophobic | % Polar |
|---|---|
| 52.21 | 47.79 |
| According to VolSite | |
| HET Code: | 024 |
|---|---|
| Formula: | C19H18BrNO5S |
| Molecular weight: | 452.319 g/mol |
| DrugBank ID: | DB06829 |
| Buried Surface Area: | 59.57 % |
| Polar Surface area: | 129.76 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 46.929 | 12.4107 | 2.3033 |
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 |
| C13 | CB | TYR- 46 | 4.22 | 0 | Hydrophobic |
| C12 | CB | ASP- 48 | 3.81 | 0 | Hydrophobic |
| C34 | CG2 | VAL- 49 | 4.33 | 0 | Hydrophobic |
| C13 | CG2 | VAL- 49 | 3.75 | 0 | Hydrophobic |
| O7 | NZ | LYS- 120 | 3.13 | 0 | Ionic (Protein Cationic) |
| O8 | NZ | LYS- 120 | 2.9 | 0 | Ionic (Protein Cationic) |
| O8 | NZ | LYS- 120 | 2.9 | 163.11 | H-Bond (Protein Donor) |
| C21 | CD1 | PHE- 182 | 3.92 | 0 | Hydrophobic |
| O26 | N | PHE- 182 | 2.75 | 145.62 | H-Bond (Protein Donor) |
| BR19 | CB | ALA- 217 | 4.14 | 0 | Hydrophobic |
| C10 | CD1 | ILE- 219 | 4.49 | 0 | Hydrophobic |
| BR19 | CG1 | ILE- 219 | 3.44 | 0 | Hydrophobic |
| C34 | CD1 | ILE- 219 | 4.08 | 0 | Hydrophobic |
| O25 | N | ARG- 221 | 3.03 | 156.64 | H-Bond (Protein Donor) |
| O25 | NE | ARG- 221 | 3.06 | 150.03 | H-Bond (Protein Donor) |
| O25 | CZ | ARG- 221 | 3.95 | 0 | Ionic (Protein Cationic) |
| C33 | SD | MET- 258 | 4.16 | 0 | Hydrophobic |
| BR19 | CB | GLN- 262 | 3.8 | 0 | Hydrophobic |
| O26 | NE2 | GLN- 266 | 2.9 | 145.31 | H-Bond (Protein Donor) |
| O25 | O | HOH- 802 | 3.04 | 179.97 | H-Bond (Protein Donor) |
