sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.900 Å
X-ray
1997-12-07
| 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: | 20.869 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.807 | 999.000 |
| % Hydrophobic | % Polar |
|---|---|
| 32.09 | 67.91 |
| According to VolSite | |
| HET Code: | GTX |
|---|---|
| Formula: | C16H28N3O6S |
| Molecular weight: | 390.475 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 52.63 % |
| 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 |
|---|---|---|
| 10.3254 | 7.04473 | 27.4874 |
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- 7 | 3.85 | 0 | Hydrophobic |
| C1S | CZ | TYR- 7 | 3.98 | 0 | Hydrophobic |
| SG2 | CE2 | PHE- 8 | 3.64 | 0 | Hydrophobic |
| C1S | CD2 | PHE- 8 | 4.45 | 0 | Hydrophobic |
| C3S | CD2 | PHE- 8 | 3.62 | 0 | Hydrophobic |
| C5S | CB | PHE- 8 | 4.1 | 0 | Hydrophobic |
| C6S | CD1 | PHE- 8 | 4.1 | 0 | Hydrophobic |
| C3S | CG2 | VAL- 10 | 4.26 | 0 | Hydrophobic |
| C5S | CG1 | VAL- 10 | 4.29 | 0 | Hydrophobic |
| O12 | CZ | ARG- 13 | 3.69 | 0 | Ionic (Protein Cationic) |
| CG1 | CD | ARG- 13 | 4.03 | 0 | Hydrophobic |
| C6S | CG2 | VAL- 35 | 3.9 | 0 | Hydrophobic |
| O31 | NE1 | TRP- 38 | 2.91 | 158.99 | H-Bond (Protein Donor) |
| O31 | NZ | LYS- 44 | 3.36 | 0 | Ionic (Protein Cationic) |
| O32 | NZ | LYS- 44 | 3.91 | 0 | Ionic (Protein Cationic) |
| CG1 | CB | GLN- 51 | 4.37 | 0 | Hydrophobic |
| O32 | NE2 | GLN- 51 | 3.15 | 172.45 | H-Bond (Protein Donor) |
| N2 | O | LEU- 52 | 2.97 | 155.94 | H-Bond (Ligand Donor) |
| O2 | N | LEU- 52 | 3 | 172.19 | H-Bond (Protein Donor) |
| N1 | OE1 | GLN- 64 | 2.72 | 160.58 | H-Bond (Ligand Donor) |
| O11 | OG | SER- 65 | 3.42 | 139.62 | H-Bond (Protein Donor) |
| O11 | N | SER- 65 | 2.86 | 165.14 | H-Bond (Protein Donor) |
| O12 | OG | SER- 65 | 2.74 | 152.3 | H-Bond (Protein Donor) |
| N1 | OD2 | ASP- 98 | 2.83 | 134.95 | H-Bond (Ligand Donor) |
| N1 | OD2 | ASP- 98 | 2.83 | 0 | Ionic (Ligand Cationic) |
| N1 | OD1 | ASP- 98 | 3.53 | 0 | Ionic (Ligand Cationic) |
| C2S | CZ | TYR- 108 | 4.15 | 0 | Hydrophobic |
| O11 | O | HOH- 222 | 3.02 | 179.98 | H-Bond (Protein Donor) |
