2.400 Å
X-ray
2007-12-01
| Name: | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial |
|---|---|
| ID: | PDK4_HUMAN |
| AC: | Q16654 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.7.11.2 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 37.485 |
|---|---|
| Number of residues: | 38 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 1.005 | 816.750 |
| % Hydrophobic | % Polar |
|---|---|
| 43.80 | 56.20 |
| According to VolSite | |

| HET Code: | ADP |
|---|---|
| Formula: | C10H12N5O10P2 |
| Molecular weight: | 424.177 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 68.81 % |
| Polar Surface area: | 260.7 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 14 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 3 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -52.8709 | 5.01385 | 26.7128 |
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 |
| N6 | OD2 | ASP- 293 | 2.74 | 161.71 | H-Bond (Ligand Donor) |
| C4' | CD2 | LEU- 306 | 3.84 | 0 | Hydrophobic |
| C1' | CD2 | LEU- 306 | 3.59 | 0 | Hydrophobic |
| C4' | CE2 | TYR- 311 | 4.19 | 0 | Hydrophobic |
| O2B | OG | SER- 312 | 2.65 | 167.14 | H-Bond (Protein Donor) |
| O3' | N | THR- 313 | 3.1 | 141.66 | H-Bond (Protein Donor) |
| O2' | OG1 | THR- 313 | 2.67 | 139.92 | H-Bond (Ligand Donor) |
| O2A | N | LEU- 334 | 3.23 | 162.24 | H-Bond (Protein Donor) |
| C5' | CD1 | LEU- 334 | 4.07 | 0 | Hydrophobic |
| O3B | MG | MG- 1500 | 2.49 | 0 | Metal Acceptor |
| O1A | MG | MG- 1500 | 2.66 | 0 | Metal Acceptor |
| N1 | O | HOH- 1503 | 2.65 | 179.95 | H-Bond (Protein Donor) |