sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
2012-07-10
| 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 |
|---|---|
| C | 39 % |
| D | 61 % |
| B-Factor: | 36.628 |
|---|---|
| Number of residues: | 41 |
| Including | |
| Standard Amino Acids: | 41 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.388 | 948.375 |
| % Hydrophobic | % Polar |
|---|---|
| 58.01 | 41.99 |
| According to VolSite | |
| HET Code: | NZT |
|---|---|
| Formula: | C24H21N6O3S |
| Molecular weight: | 473.527 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 63.25 % |
| Polar Surface area: | 118.84 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 0 |
| Rings: | 5 |
| Aromatic rings: | 4 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| -19.465 | -10.33 | 27.3396 |
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 |
| CAO | CB | PHE- 26 | 4.12 | 0 | Hydrophobic |
| CAT | CE1 | PHE- 26 | 4.18 | 0 | Hydrophobic |
| CAT | CE2 | PHE- 26 | 3.38 | 0 | Hydrophobic |
| CAI | CZ | PHE- 26 | 3.26 | 0 | Hydrophobic |
| CAN | CB | LEU- 27 | 4.46 | 0 | Hydrophobic |
| CAD | CD1 | LEU- 27 | 4.37 | 0 | Hydrophobic |
| CAL | SD | MET- 30 | 4.13 | 0 | Hydrophobic |
| CAS | CE | MET- 30 | 3.72 | 0 | Hydrophobic |
| CAT | SD | MET- 30 | 4.2 | 0 | Hydrophobic |
| OAA | NZ | LYS- 311 | 2.54 | 154.96 | H-Bond (Protein Donor) |
| NAX | O | LEU- 353 | 2.85 | 155.27 | H-Bond (Ligand Donor) |
| CAJ | CD2 | LEU- 353 | 3.61 | 0 | Hydrophobic |
| CAL | CD1 | LEU- 353 | 4.06 | 0 | Hydrophobic |
| CAZ | CB | LEU- 353 | 3.68 | 0 | Hydrophobic |
| CAI | CB | TYR- 390 | 3.74 | 0 | Hydrophobic |
| CAE | CG | GLN- 393 | 3.85 | 0 | Hydrophobic |
| CBD | CD1 | LEU- 394 | 4.13 | 0 | Hydrophobic |
| CAI | CB | LEU- 394 | 4.26 | 0 | Hydrophobic |
