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
2003-08-13
| 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 | 76 % |
| B | 24 % |
| B-Factor: | 27.479 |
|---|---|
| Number of residues: | 43 |
| Including | |
| Standard Amino Acids: | 38 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 4 |
| Cofactors: | |
| Metals: | CL |
| Ligandability | Volume (Å3) |
|---|---|
| 0.881 | 1032.750 |
| % Hydrophobic | % Polar |
|---|---|
| 39.54 | 60.46 |
| According to VolSite | |
| HET Code: | P90 |
|---|---|
| Formula: | C31H23F2N4O3PS |
| Molecular weight: | 600.575 g/mol |
| DrugBank ID: | DB04285 |
| Buried Surface Area: | 75.55 % |
| Polar Surface area: | 144.84 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 0 |
| Rings: | 6 |
| Aromatic rings: | 6 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| 7.79774 | 42.8034 | 18.1483 |
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 |
| C1 | CD1 | TYR- 546 | 4.49 | 0 | Hydrophobic |
| C32 | CG | TYR- 546 | 3.45 | 0 | Hydrophobic |
| C4B | CZ | TYR- 546 | 3.47 | 0 | Hydrophobic |
| C8A | CB | ARG- 547 | 4.06 | 0 | Hydrophobic |
| N63 | N | ASP- 548 | 2.99 | 161.3 | H-Bond (Protein Donor) |
| C1B | CB | ASP- 548 | 3.93 | 0 | Hydrophobic |
| C4A | CG2 | VAL- 549 | 3.82 | 0 | Hydrophobic |
| C1B | CG2 | VAL- 549 | 3.77 | 0 | Hydrophobic |
| C58 | CB | SER- 618 | 3.7 | 0 | Hydrophobic |
| F38 | CD2 | LEU- 619 | 4.19 | 0 | Hydrophobic |
| C5B | CD2 | LEU- 619 | 3.9 | 0 | Hydrophobic |
| C57 | CD1 | LEU- 619 | 3.71 | 0 | Hydrophobic |
| F38 | CB | ASP- 681 | 4.31 | 0 | Hydrophobic |
| F39 | CD1 | PHE- 682 | 3.55 | 0 | Hydrophobic |
| S52 | CZ | PHE- 682 | 3.65 | 0 | Hydrophobic |
| C36 | CZ | PHE- 682 | 3.43 | 0 | Hydrophobic |
| O42 | N | SER- 716 | 2.82 | 134.8 | H-Bond (Protein Donor) |
| O42 | N | ALA- 717 | 2.67 | 167.1 | H-Bond (Protein Donor) |
| C4A | CB | ALA- 717 | 3.37 | 0 | Hydrophobic |
| C36 | CB | ALA- 717 | 3.33 | 0 | Hydrophobic |
| O41 | N | ILE- 719 | 3.07 | 155.81 | H-Bond (Protein Donor) |
| C5A | CD1 | ILE- 719 | 3.76 | 0 | Hydrophobic |
| C1A | CD1 | ILE- 719 | 3.93 | 0 | Hydrophobic |
| O41 | N | GLY- 720 | 2.65 | 168.87 | H-Bond (Protein Donor) |
| O42 | NH2 | ARG- 721 | 3.03 | 149.22 | H-Bond (Protein Donor) |
| O43 | NH2 | ARG- 721 | 3.39 | 133.03 | H-Bond (Protein Donor) |
| O43 | N | ARG- 721 | 3.08 | 168.77 | H-Bond (Protein Donor) |
| O43 | NE | ARG- 721 | 2.79 | 166.72 | H-Bond (Protein Donor) |
| O42 | CZ | ARG- 721 | 3.92 | 0 | Ionic (Protein Cationic) |
| O43 | CZ | ARG- 721 | 3.54 | 0 | Ionic (Protein Cationic) |
| C2B | SD | MET- 758 | 3.72 | 0 | Hydrophobic |
| C5A | CG | GLN- 762 | 4.26 | 0 | Hydrophobic |
| F39 | CG | GLN- 762 | 3.51 | 0 | Hydrophobic |
| C56 | CB | ALA- 1018 | 3.93 | 0 | Hydrophobic |
| S52 | CB | GLN- 1021 | 4.11 | 0 | Hydrophobic |
| C56 | CB | ASP- 1022 | 3.72 | 0 | Hydrophobic |
| C12 | CB | HIS- 1025 | 4.34 | 0 | Hydrophobic |
| C8B | CB | HIS- 1025 | 3.46 | 0 | Hydrophobic |
| C9B | CB | HIS- 1025 | 3.66 | 0 | Hydrophobic |
| C9B | CG | GLU- 1026 | 3.73 | 0 | Hydrophobic |
| O43 | O | HOH- 2001 | 2.61 | 179.99 | H-Bond (Protein Donor) |
