sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.400 Å
X-ray
2011-01-16
| Name: | Receptor-type tyrosine-protein phosphatase gamma |
|---|---|
| ID: | PTPRG_HUMAN |
| AC: | P23470 |
| 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: | 44.767 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 29 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.238 | 445.500 |
| % Hydrophobic | % Polar |
|---|---|
| 63.64 | 36.36 |
| According to VolSite | |
| HET Code: | NXV |
|---|---|
| Formula: | C18H13Cl2O3S |
| Molecular weight: | 380.265 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 65.09 % |
| Polar Surface area: | 85.66 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 1 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 18.7677 | 29.1419 | 61.5705 |
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 |
| CL18 | CD1 | ILE- 950 | 4.36 | 0 | Hydrophobic |
| C15 | CG2 | ILE- 950 | 3.42 | 0 | Hydrophobic |
| C14 | CB | TYR- 1023 | 4.49 | 0 | Hydrophobic |
| CL19 | CG | TYR- 1023 | 3.96 | 0 | Hydrophobic |
| S10 | CZ3 | TRP- 1026 | 3.98 | 0 | Hydrophobic |
| C13 | CH2 | TRP- 1026 | 3.2 | 0 | Hydrophobic |
| C1 | CG1 | VAL- 1031 | 3.68 | 0 | Hydrophobic |
| C3 | CG1 | VAL- 1031 | 3.51 | 0 | Hydrophobic |
| C4 | CG2 | VAL- 1031 | 3.47 | 0 | Hydrophobic |
| C6 | CB | PRO- 1032 | 4.05 | 0 | Hydrophobic |
| C5 | CG | PRO- 1032 | 4.06 | 0 | Hydrophobic |
| C11 | CG | PRO- 1032 | 3.59 | 0 | Hydrophobic |
| CL18 | CG1 | VAL- 1038 | 3.76 | 0 | Hydrophobic |
| C14 | CG2 | VAL- 1038 | 3.49 | 0 | Hydrophobic |
| C15 | CG1 | VAL- 1038 | 3.43 | 0 | Hydrophobic |
| C16 | CG1 | VAL- 1038 | 3.39 | 0 | Hydrophobic |
| CL19 | CE2 | PHE- 1041 | 3.38 | 0 | Hydrophobic |
| S10 | CG | ARG- 1066 | 3.79 | 0 | Hydrophobic |
| O21 | NE | ARG- 1066 | 2.93 | 130.78 | H-Bond (Protein Donor) |
| O21 | NH2 | ARG- 1066 | 3.1 | 124.92 | H-Bond (Protein Donor) |
| O22 | NE | ARG- 1066 | 3.34 | 171.1 | H-Bond (Protein Donor) |
| O21 | CZ | ARG- 1066 | 3.37 | 0 | Ionic (Protein Cationic) |
| C17 | CG2 | THR- 1069 | 3.76 | 0 | Hydrophobic |
| CL18 | CB | TYR- 1070 | 3.74 | 0 | Hydrophobic |
| CL18 | CD1 | ILE- 1073 | 4.2 | 0 | Hydrophobic |
| C23 | CB | GLU- 1107 | 4.27 | 0 | Hydrophobic |
| C2 | CB | GLU- 1107 | 3.84 | 0 | Hydrophobic |
| C7 | CB | GLU- 1107 | 4.24 | 0 | Hydrophobic |
| O22 | NE2 | GLN- 1108 | 2.79 | 149.03 | H-Bond (Protein Donor) |
| C5 | CG | GLN- 1108 | 4.01 | 0 | Hydrophobic |
| C23 | CG2 | ILE- 1110 | 3.61 | 0 | Hydrophobic |
| C11 | CE2 | PHE- 1111 | 3.65 | 0 | Hydrophobic |
| C6 | CB | PHE- 1111 | 4.02 | 0 | Hydrophobic |
| C8 | CB | PHE- 1111 | 3.72 | 0 | Hydrophobic |
