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: | 39.321 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.644 | 546.750 |
| % Hydrophobic | % Polar |
|---|---|
| 54.32 | 45.68 |
| According to VolSite | |
| HET Code: | NXW |
|---|---|
| Formula: | C27H25Cl2N3O3S |
| Molecular weight: | 542.477 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 57.1 % |
| Polar Surface area: | 123.17 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 1 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 12 |
| X | Y | Z |
|---|---|---|
| 23.0633 | 25.8052 | 26.0907 |
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 |
| CL35 | CG2 | ILE- 950 | 3.45 | 0 | Hydrophobic |
| C19 | CG2 | ILE- 950 | 3.51 | 0 | Hydrophobic |
| CL35 | CG | TYR- 1023 | 4.08 | 0 | Hydrophobic |
| C7 | CH2 | TRP- 1026 | 3.23 | 0 | Hydrophobic |
| S34 | CZ3 | TRP- 1026 | 4.27 | 0 | Hydrophobic |
| C6 | CG1 | VAL- 1031 | 3.9 | 0 | Hydrophobic |
| C5 | CB | VAL- 1031 | 3.47 | 0 | Hydrophobic |
| C24 | CG | PRO- 1032 | 3.89 | 0 | Hydrophobic |
| C11 | CG | PRO- 1032 | 3.98 | 0 | Hydrophobic |
| CL36 | CG1 | VAL- 1038 | 3.96 | 0 | Hydrophobic |
| C7 | CG2 | VAL- 1038 | 3.56 | 0 | Hydrophobic |
| C19 | CG1 | VAL- 1038 | 3.48 | 0 | Hydrophobic |
| CL35 | CD2 | PHE- 1041 | 3.35 | 0 | Hydrophobic |
| O31 | NE | ARG- 1066 | 2.81 | 139.41 | H-Bond (Protein Donor) |
| O31 | NH2 | ARG- 1066 | 2.82 | 135.61 | H-Bond (Protein Donor) |
| O33 | NE | ARG- 1066 | 3.48 | 153.83 | H-Bond (Protein Donor) |
| O31 | CZ | ARG- 1066 | 3.2 | 0 | Ionic (Protein Cationic) |
| S34 | CG | ARG- 1066 | 3.72 | 0 | Hydrophobic |
| CL36 | CG2 | THR- 1069 | 3.8 | 0 | Hydrophobic |
| C12 | CG2 | THR- 1069 | 3.69 | 0 | Hydrophobic |
| CL35 | CD1 | TYR- 1070 | 4.44 | 0 | Hydrophobic |
| CL36 | CB | TYR- 1070 | 3.69 | 0 | Hydrophobic |
| CL36 | CD1 | ILE- 1073 | 4.33 | 0 | Hydrophobic |
| N29 | OE1 | GLU- 1106 | 3.9 | 0 | Ionic (Ligand Cationic) |
| C10 | CB | GLU- 1107 | 4.41 | 0 | Hydrophobic |
| C2 | CB | GLU- 1107 | 4.07 | 0 | Hydrophobic |
| C5 | CB | GLU- 1107 | 4.04 | 0 | Hydrophobic |
| N29 | OE2 | GLU- 1107 | 3.28 | 0 | Ionic (Ligand Cationic) |
| O33 | NE2 | GLN- 1108 | 2.82 | 149.14 | H-Bond (Protein Donor) |
| S34 | CG | GLN- 1108 | 4.2 | 0 | Hydrophobic |
| C18 | CG | GLN- 1108 | 3.96 | 0 | Hydrophobic |
| C10 | CB | ILE- 1110 | 4.45 | 0 | Hydrophobic |
| C8 | CG2 | ILE- 1110 | 3.68 | 0 | Hydrophobic |
| C24 | CE2 | PHE- 1111 | 3.83 | 0 | Hydrophobic |
| C1 | CB | PHE- 1111 | 3.69 | 0 | Hydrophobic |
| C4 | CB | PHE- 1111 | 3.69 | 0 | Hydrophobic |
| C11 | CB | PHE- 1111 | 4.02 | 0 | Hydrophobic |
| C3 | CB | ASP- 1114 | 4.35 | 0 | Hydrophobic |
