sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.750 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: | 27.816 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.869 | 334.125 |
| % Hydrophobic | % Polar |
|---|---|
| 58.59 | 41.41 |
| According to VolSite | |
| HET Code: | PV1 |
|---|---|
| Formula: | C15H12BrNO3 |
| Molecular weight: | 334.165 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 60.88 % |
| Polar Surface area: | 60.77 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 1 |
| X | Y | Z |
|---|---|---|
| 14.0035 | 2.2079 | -37.6658 |
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 |
| C15 | CB | ASN- 255 | 4.4 | 0 | Hydrophobic |
| C14 | CB | ASN- 255 | 3.75 | 0 | Hydrophobic |
| C13 | CB | ASN- 255 | 3.38 | 0 | Hydrophobic |
| C12 | CB | ALA- 256 | 4.34 | 0 | Hydrophobic |
| C6 | CG | ARG- 258 | 3.73 | 0 | Hydrophobic |
| C11 | CB | ALA- 259 | 4.21 | 0 | Hydrophobic |
| C3 | CB | ALA- 259 | 3.49 | 0 | Hydrophobic |
| C1 | CB | GLU- 262 | 4.09 | 0 | Hydrophobic |
| C15 | CG2 | VAL- 295 | 4.48 | 0 | Hydrophobic |
| BR1 | CD1 | LEU- 303 | 3.66 | 0 | Hydrophobic |
| BR1 | CG | LEU- 330 | 4.12 | 0 | Hydrophobic |
| BR1 | CD1 | LEU- 346 | 3.43 | 0 | Hydrophobic |
| O1 | OG1 | THR- 354 | 2.83 | 127.59 | H-Bond (Protein Donor) |
| C12 | CG2 | THR- 354 | 4.15 | 0 | Hydrophobic |
| C11 | CB | THR- 354 | 3.74 | 0 | Hydrophobic |
