sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.700 Å
X-ray
2013-09-12
| Name: | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial |
|---|---|
| ID: | PDK2_HUMAN |
| AC: | Q15119 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.7.11.2 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 25.820 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.748 | 307.125 |
| % Hydrophobic | % Polar |
|---|---|
| 52.75 | 47.25 |
| According to VolSite | |
| HET Code: | PV2 |
|---|---|
| Formula: | C14H11NO4S |
| Molecular weight: | 289.306 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 64.37 % |
| Polar Surface area: | 91.88 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 0 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| 13.8892 | 2.1131 | -37.2976 |
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 |
| C6 | CB | ASN- 255 | 3.73 | 0 | Hydrophobic |
| C5 | CB | ASN- 255 | 3.4 | 0 | Hydrophobic |
| C13 | CG | ARG- 258 | 3.69 | 0 | Hydrophobic |
| C10 | CB | ALA- 259 | 3.65 | 0 | Hydrophobic |
| C7 | CB | ALA- 259 | 3.5 | 0 | Hydrophobic |
| C8 | CB | ALA- 259 | 3.41 | 0 | Hydrophobic |
| C9 | CB | ALA- 259 | 3.49 | 0 | Hydrophobic |
| C12 | CB | GLU- 262 | 3.93 | 0 | Hydrophobic |
| O1 | OD1 | ASP- 290 | 3.4 | 124.25 | H-Bond (Ligand Donor) |
| O1 | OD2 | ASP- 290 | 2.51 | 164.36 | H-Bond (Ligand Donor) |
| C1 | CD1 | LEU- 303 | 3.87 | 0 | Hydrophobic |
| C6 | CD1 | LEU- 330 | 4.23 | 0 | Hydrophobic |
| C5 | CD2 | LEU- 346 | 4.28 | 0 | Hydrophobic |
| C6 | CD1 | LEU- 346 | 4.04 | 0 | Hydrophobic |
| C2 | CG2 | THR- 354 | 4.17 | 0 | Hydrophobic |
| C3 | CB | THR- 354 | 3.72 | 0 | Hydrophobic |
| C4 | CG2 | THR- 354 | 3.98 | 0 | Hydrophobic |
| O3 | OG1 | THR- 354 | 2.82 | 158.98 | H-Bond (Protein Donor) |
| O3 | O | HOH- 602 | 3.1 | 179.98 | H-Bond (Protein Donor) |
