sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.500 Å
X-ray
2011-01-16
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 5.600 | 5.600 | 5.600 | 0.000 | 5.600 | 1 |
| 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 |
|---|---|
| B | 100 % |
| B-Factor: | 31.294 |
|---|---|
| Number of residues: | 23 |
| Including | |
| Standard Amino Acids: | 23 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.074 | 300.375 |
| % Hydrophobic | % Polar |
|---|---|
| 80.90 | 19.10 |
| According to VolSite | |
| HET Code: | NXY |
|---|---|
| Formula: | C12H7Cl2O2S2 |
| Molecular weight: | 318.219 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 70.12 % |
| Polar Surface area: | 93.66 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 0 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 32.5852 | 56.4528 | 78.1089 |
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 |
| CL17 | CD1 | ILE- 950 | 4.21 | 0 | Hydrophobic |
| CL18 | CG2 | ILE- 950 | 3.7 | 0 | Hydrophobic |
| C16 | CG2 | ILE- 950 | 3.59 | 0 | Hydrophobic |
| CL18 | CD1 | TYR- 1023 | 4.05 | 0 | Hydrophobic |
| S3 | CZ3 | TRP- 1026 | 3.61 | 0 | Hydrophobic |
| S5 | CG1 | VAL- 1031 | 3.49 | 0 | Hydrophobic |
| C13 | CG | PRO- 1032 | 3.86 | 0 | Hydrophobic |
| CL17 | CG1 | VAL- 1038 | 3.93 | 0 | Hydrophobic |
| C13 | CG2 | VAL- 1038 | 3.44 | 0 | Hydrophobic |
| C16 | CG1 | VAL- 1038 | 3.43 | 0 | Hydrophobic |
| CL18 | CD2 | PHE- 1041 | 3.3 | 0 | Hydrophobic |
| S3 | CG | ARG- 1066 | 4.13 | 0 | Hydrophobic |
| O10 | NE | ARG- 1066 | 2.91 | 168.76 | H-Bond (Protein Donor) |
| O10 | CZ | ARG- 1066 | 3.7 | 0 | Ionic (Protein Cationic) |
| C12 | CG2 | THR- 1069 | 3.96 | 0 | Hydrophobic |
| CL17 | CG2 | THR- 1069 | 4 | 0 | Hydrophobic |
| CL17 | CB | TYR- 1070 | 3.53 | 0 | Hydrophobic |
| CL18 | CD1 | TYR- 1070 | 4.38 | 0 | Hydrophobic |
| CL17 | CD1 | ILE- 1073 | 4.36 | 0 | Hydrophobic |
| S5 | CB | GLU- 1107 | 3.78 | 0 | Hydrophobic |
| S5 | CG | GLN- 1108 | 4.07 | 0 | Hydrophobic |
| O9 | NE2 | GLN- 1108 | 3.38 | 139.64 | H-Bond (Protein Donor) |
| C7 | CE2 | PHE- 1111 | 3.52 | 0 | Hydrophobic |
