sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.800 Å
X-ray
2008-01-28
| Name: | Phosphoglycerate kinase 1 |
|---|---|
| ID: | PGK1_HUMAN |
| AC: | P00558 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.7.2.3 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 22.836 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.918 | 293.625 |
| % Hydrophobic | % Polar |
|---|---|
| 70.11 | 29.89 |
| According to VolSite | |
| HET Code: | CDP |
|---|---|
| Formula: | C9H12N3O11P2 |
| Molecular weight: | 400.153 g/mol |
| DrugBank ID: | DB04555 |
| Buried Surface Area: | 46.12 % |
| Polar Surface area: | 249.77 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 13 |
| H-Bond Donors: | 3 |
| Rings: | 2 |
| Aromatic rings: | 0 |
| Anionic atoms: | 3 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -6.7018 | -0.14464 | -35.8661 |
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 |
| O1B | N | ALA- 214 | 2.86 | 163.65 | H-Bond (Protein Donor) |
| C2' | CB | ALA- 214 | 3.79 | 0 | Hydrophobic |
| O1B | NZ | LYS- 219 | 3.63 | 0 | Ionic (Protein Cationic) |
| C3' | CG | PRO- 338 | 3.9 | 0 | Hydrophobic |
| C4' | CG | PRO- 338 | 3.48 | 0 | Hydrophobic |
| O3' | O | PRO- 338 | 3.01 | 122.83 | H-Bond (Ligand Donor) |
| C1' | CG2 | VAL- 341 | 3.7 | 0 | Hydrophobic |
