sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.270 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: | 43.694 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.436 | 533.250 |
| % Hydrophobic | % Polar |
|---|---|
| 65.19 | 34.81 |
| According to VolSite | |
| HET Code: | NX3 |
|---|---|
| Formula: | C18H14Cl2N2O3S3 |
| Molecular weight: | 473.416 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 63.94 % |
| Polar Surface area: | 151.17 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 21.1027 | 30.5685 | 60.9945 |
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 |
| CL19 | CG2 | ILE- 950 | 3.72 | 0 | Hydrophobic |
| C15 | CG2 | ILE- 950 | 3.61 | 0 | Hydrophobic |
| C14 | CB | TYR- 1023 | 4.44 | 0 | Hydrophobic |
| CL19 | CG | TYR- 1023 | 4.04 | 0 | Hydrophobic |
| S10 | CZ3 | TRP- 1026 | 3.99 | 0 | Hydrophobic |
| C13 | CH2 | TRP- 1026 | 3.4 | 0 | Hydrophobic |
| S1 | CB | VAL- 1031 | 3.65 | 0 | Hydrophobic |
| S10 | CG | PRO- 1032 | 3.66 | 0 | Hydrophobic |
| C11 | CB | PRO- 1032 | 3.82 | 0 | Hydrophobic |
| CL18 | CG1 | VAL- 1038 | 3.8 | 0 | Hydrophobic |
| C13 | CG2 | VAL- 1038 | 3.76 | 0 | Hydrophobic |
| C15 | CG1 | VAL- 1038 | 3.57 | 0 | Hydrophobic |
| C16 | CG1 | VAL- 1038 | 3.42 | 0 | Hydrophobic |
| CL19 | CE2 | PHE- 1041 | 3.39 | 0 | Hydrophobic |
| CL18 | CG2 | VAL- 1042 | 4.25 | 0 | Hydrophobic |
| O8 | NH1 | ARG- 1066 | 3.35 | 145.59 | H-Bond (Protein Donor) |
| O21 | NH1 | ARG- 1066 | 2.55 | 122.52 | H-Bond (Protein Donor) |
| S10 | CG | ARG- 1066 | 3.6 | 0 | Hydrophobic |
| C23 | CD | ARG- 1066 | 3.95 | 0 | Hydrophobic |
| C17 | CG2 | THR- 1069 | 3.72 | 0 | Hydrophobic |
| CL18 | CB | TYR- 1070 | 3.59 | 0 | Hydrophobic |
| CL19 | CD1 | TYR- 1070 | 4.45 | 0 | Hydrophobic |
| CL18 | CD1 | ILE- 1073 | 4.19 | 0 | Hydrophobic |
| C25 | CG | GLN- 1104 | 4.3 | 0 | Hydrophobic |
| C26 | CG2 | THR- 1105 | 4.04 | 0 | Hydrophobic |
| S1 | CB | GLU- 1107 | 3.74 | 0 | Hydrophobic |
| S1 | CG | GLN- 1108 | 3.77 | 0 | Hydrophobic |
| C11 | CE2 | PHE- 1111 | 3.5 | 0 | Hydrophobic |
