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
2006-11-08
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 5.000 | 5.000 | 5.000 | 0.000 | 5.000 | 1 |
| Name: | Glutathione S-transferase P |
|---|---|
| ID: | GSTP1_HUMAN |
| AC: | P09211 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.5.1.18 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 93 % |
| B | 7 % |
| B-Factor: | 34.528 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.320 | 475.875 |
| % Hydrophobic | % Polar |
|---|---|
| 39.01 | 60.99 |
| According to VolSite | |
| HET Code: | GTX |
|---|---|
| Formula: | C16H28N3O6S |
| Molecular weight: | 390.475 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 53.03 % |
| Polar Surface area: | 191.4 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 3 |
| Rings: | 0 |
| Aromatic rings: | 0 |
| Anionic atoms: | 2 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 15 |
| X | Y | Z |
|---|---|---|
| 9.58992 | -2.515 | 7.56781 |
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 |
| SG2 | CE1 | TYR- 8 | 3.96 | 0 | Hydrophobic |
| SG2 | CE2 | PHE- 9 | 3.5 | 0 | Hydrophobic |
| C4S | CG | PHE- 9 | 4.41 | 0 | Hydrophobic |
| C5S | CB | PHE- 9 | 4.03 | 0 | Hydrophobic |
| C3S | CD2 | PHE- 9 | 3.45 | 0 | Hydrophobic |
| C5S | CG1 | VAL- 11 | 4.06 | 0 | Hydrophobic |
| C3S | CG2 | VAL- 11 | 4.01 | 0 | Hydrophobic |
| O11 | CZ | ARG- 14 | 3.42 | 0 | Ionic (Protein Cationic) |
| CG1 | CD | ARG- 14 | 4.01 | 0 | Hydrophobic |
| C6S | CG2 | VAL- 36 | 3.44 | 0 | Hydrophobic |
| O31 | NE1 | TRP- 39 | 3.08 | 166.19 | H-Bond (Protein Donor) |
| O31 | NZ | LYS- 45 | 2.98 | 169.41 | H-Bond (Protein Donor) |
| O32 | NZ | LYS- 45 | 3.31 | 134.4 | H-Bond (Protein Donor) |
| O31 | NZ | LYS- 45 | 2.98 | 0 | Ionic (Protein Cationic) |
| O32 | NZ | LYS- 45 | 3.31 | 0 | Ionic (Protein Cationic) |
| CG1 | CB | GLN- 52 | 4.32 | 0 | Hydrophobic |
| O32 | NE2 | GLN- 52 | 3.05 | 161.98 | H-Bond (Protein Donor) |
| N2 | O | LEU- 53 | 2.58 | 159.05 | H-Bond (Ligand Donor) |
| O2 | N | LEU- 53 | 2.61 | 172.68 | H-Bond (Protein Donor) |
| N1 | OE1 | GLN- 65 | 2.67 | 151.43 | H-Bond (Ligand Donor) |
| O12 | N | SER- 66 | 2.74 | 146.94 | H-Bond (Protein Donor) |
| O12 | OG | SER- 66 | 3.28 | 141.58 | H-Bond (Protein Donor) |
| N1 | OD2 | ASP- 99 | 2.78 | 129.25 | H-Bond (Ligand Donor) |
| N1 | OD2 | ASP- 99 | 2.78 | 0 | Ionic (Ligand Cationic) |
| N1 | OD1 | ASP- 99 | 3.56 | 0 | Ionic (Ligand Cationic) |
| C2S | CZ | TYR- 109 | 4.35 | 0 | Hydrophobic |
| O12 | O | HOH- 2011 | 2.81 | 179.94 | H-Bond (Protein Donor) |
