sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.990 Å
X-ray
2011-06-17
| Name: | Serine-pyruvate aminotransferase (AgxT) |
|---|---|
| ID: | Q97VM5_SULSO |
| AC: | Q97VM5 |
| Organism: | Sulfolobus solfataricus |
| Reign: | Archaea |
| TaxID: | 273057 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 82 % |
| B | 18 % |
| B-Factor: | 33.286 |
|---|---|
| Number of residues: | 39 |
| Including | |
| Standard Amino Acids: | 38 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.059 | 594.000 |
| % Hydrophobic | % Polar |
|---|---|
| 65.34 | 34.66 |
| According to VolSite | |
| HET Code: | PXG |
|---|---|
| Formula: | C15H14N2O7P |
| Molecular weight: | 365.255 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 73.19 % |
| Polar Surface area: | 167.51 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 9 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 3 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| -22.0526 | -19.8464 | -16.774 |
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 |
| C13 | CG1 | VAL- 8 | 4 | 0 | Hydrophobic |
| C12 | CE1 | PHE- 28 | 3.35 | 0 | Hydrophobic |
| OP1 | N | GLY- 63 | 2.87 | 146.67 | H-Bond (Protein Donor) |
| OP3 | OG1 | THR- 64 | 2.51 | 149.3 | H-Bond (Protein Donor) |
| OP3 | N | THR- 64 | 2.64 | 148.23 | H-Bond (Protein Donor) |
| C2A | CB | PHE- 88 | 3.76 | 0 | Hydrophobic |
| C3 | CB | PHE- 88 | 4.32 | 0 | Hydrophobic |
| C5A | CE1 | PHE- 88 | 3.88 | 0 | Hydrophobic |
| C4A | CE1 | PHE- 88 | 3.7 | 0 | Hydrophobic |
| DuAr | DuAr | PHE- 88 | 3.77 | 0 | Aromatic Face/Face |
| C2A | CG2 | THR- 134 | 4.19 | 0 | Hydrophobic |
| C2A | CB | THR- 138 | 4.38 | 0 | Hydrophobic |
| C3 | CB | THR- 138 | 4.45 | 0 | Hydrophobic |
| C9 | CG2 | THR- 138 | 3.94 | 0 | Hydrophobic |
| O3 | OG1 | THR- 138 | 2.54 | 141.69 | H-Bond (Ligand Donor) |
| N1 | OD2 | ASP- 163 | 2.59 | 172.18 | H-Bond (Ligand Donor) |
| C2A | CB | VAL- 165 | 3.96 | 0 | Hydrophobic |
| C4A | CG1 | VAL- 165 | 4.1 | 0 | Hydrophobic |
| C3 | CG1 | VAL- 165 | 3.47 | 0 | Hydrophobic |
| O3 | OG | SER- 166 | 3.43 | 126.31 | H-Bond (Ligand Donor) |
| OP1 | NE2 | GLN- 188 | 2.97 | 154.22 | H-Bond (Protein Donor) |
| OP2 | OH | TYR- 240 | 2.76 | 174.44 | H-Bond (Protein Donor) |
| C12 | CE1 | TYR- 240 | 3.31 | 0 | Hydrophobic |
| OP2 | N | THR- 243 | 2.84 | 152.15 | H-Bond (Protein Donor) |
| OP2 | OG1 | THR- 243 | 2.73 | 152.47 | H-Bond (Protein Donor) |
| O2 | NH2 | ARG- 337 | 3.26 | 139.13 | H-Bond (Protein Donor) |
| O8 | NH2 | ARG- 337 | 2.88 | 156.25 | H-Bond (Protein Donor) |
| O8 | NH1 | ARG- 337 | 3.17 | 138.69 | H-Bond (Protein Donor) |
| O8 | CZ | ARG- 337 | 3.45 | 0 | Ionic (Protein Cationic) |
