sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.330 Å
X-ray
2013-03-19
| Name: | Pyruvate kinase PKM |
|---|---|
| ID: | KPYM_HUMAN |
| AC: | P14618 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.7.1.40 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 58 % |
| B | 42 % |
| B-Factor: | 40.816 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.343 | 708.750 |
| % Hydrophobic | % Polar |
|---|---|
| 69.52 | 30.48 |
| According to VolSite | |
| HET Code: | 1OX |
|---|---|
| Formula: | C16H12N4O |
| Molecular weight: | 276.293 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 61.1 % |
| Polar Surface area: | 50.49 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 0 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| 8.87548 | 2.99929 | 10.7889 |
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 |
| C16 | CE1 | PHE- 26 | 4.18 | 0 | Hydrophobic |
| C3 | CG | MET- 30 | 4.49 | 0 | Hydrophobic |
| C1 | CD1 | LEU- 33 | 4.23 | 0 | Hydrophobic |
| C3 | CD | LYS- 311 | 3.63 | 0 | Hydrophobic |
| N17 | NZ | LYS- 311 | 2.88 | 154.22 | H-Bond (Protein Donor) |
| C3 | CD1 | LEU- 353 | 3.73 | 0 | Hydrophobic |
| C7 | CB | LEU- 353 | 3.98 | 0 | Hydrophobic |
| C16 | CB | LEU- 353 | 4.46 | 0 | Hydrophobic |
| C2 | CD2 | LEU- 353 | 3.62 | 0 | Hydrophobic |
| C2 | CB | TYR- 390 | 4.39 | 0 | Hydrophobic |
