sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.550 Å
X-ray
2012-07-03
| 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 |
|---|---|
| D | 100 % |
| B-Factor: | 50.720 |
|---|---|
| Number of residues: | 47 |
| Including | |
| Standard Amino Acids: | 43 |
| Non Standard Amino Acids: | 3 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | K MG MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.484 | 955.125 |
| % Hydrophobic | % Polar |
|---|---|
| 44.17 | 55.83 |
| According to VolSite | |
| HET Code: | ATP |
|---|---|
| Formula: | C10H12N5O13P3 |
| Molecular weight: | 503.149 g/mol |
| DrugBank ID: | DB00171 |
| Buried Surface Area: | 63.93 % |
| Polar Surface area: | 319.88 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 17 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| -4.54319 | -26.1861 | 130.754 |
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 |
| O1A | CZ | ARG- 73 | 3.58 | 0 | Ionic (Protein Cationic) |
| O2A | NH2 | ARG- 73 | 3.12 | 133.67 | H-Bond (Protein Donor) |
| O3B | ND2 | ASN- 75 | 3.15 | 147.97 | H-Bond (Protein Donor) |
| O1B | NE2 | HIS- 78 | 3.22 | 168.91 | H-Bond (Protein Donor) |
| O1B | CZ | ARG- 120 | 3.85 | 0 | Ionic (Protein Cationic) |
| O3' | NZ | LYS- 207 | 2.66 | 125.75 | H-Bond (Protein Donor) |
| O2' | NZ | LYS- 207 | 3.34 | 159.33 | H-Bond (Protein Donor) |
| O1G | NZ | LYS- 270 | 3.62 | 0 | Ionic (Protein Cationic) |
| O2A | OG | SER- 362 | 3.37 | 123.04 | H-Bond (Protein Donor) |
| C1' | CB | ALA- 366 | 4.3 | 0 | Hydrophobic |
| C4' | CD | LYS- 367 | 4.25 | 0 | Hydrophobic |
| C1' | CD | LYS- 367 | 4.09 | 0 | Hydrophobic |
| O2G | MG | MG- 603 | 2.27 | 0 | Metal Acceptor |
| O3G | MG | MG- 605 | 2.73 | 0 | Metal Acceptor |
| O2B | MG | MG- 605 | 1.98 | 0 | Metal Acceptor |
| O2A | MG | MG- 605 | 1.99 | 0 | Metal Acceptor |
