sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.400 Å
X-ray
2005-06-08
| 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: | 55.477 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.183 | 408.375 |
| % Hydrophobic | % Polar |
|---|---|
| 63.64 | 36.36 |
| According to VolSite | |
| HET Code: | TF3 |
|---|---|
| Formula: | C20H26ClN2O2 |
| Molecular weight: | 361.886 g/mol |
| DrugBank ID: | DB08610 |
| Buried Surface Area: | 54.51 % |
| Polar Surface area: | 65.97 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 37.9274 | 35.2504 | 90.3348 |
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 |
| CL1 | CD2 | LEU- 63 | 3.67 | 0 | Hydrophobic |
| C11 | CD2 | LEU- 63 | 3.69 | 0 | Hydrophobic |
| CL1 | CG | PRO- 64 | 3.82 | 0 | Hydrophobic |
| C2 | CG | PRO- 64 | 3.63 | 0 | Hydrophobic |
| O2 | NH2 | ARG- 66 | 3.46 | 151.34 | H-Bond (Protein Donor) |
| C6 | CG2 | VAL- 67 | 3.61 | 0 | Hydrophobic |
| C15 | CG1 | VAL- 67 | 3.61 | 0 | Hydrophobic |
| C19 | CG2 | VAL- 73 | 3.76 | 0 | Hydrophobic |
| C19 | SD | MET- 122 | 4.4 | 0 | Hydrophobic |
| C19 | CG2 | VAL- 126 | 4.45 | 0 | Hydrophobic |
| C20 | CG2 | VAL- 126 | 3.6 | 0 | Hydrophobic |
| C6 | CE2 | TYR- 129 | 3.79 | 0 | Hydrophobic |
| C10 | CB | TYR- 129 | 4 | 0 | Hydrophobic |
| CL1 | CB | ASN- 142 | 3.96 | 0 | Hydrophobic |
| C2 | CB | ASN- 142 | 3.45 | 0 | Hydrophobic |
| C8 | CG1 | ILE- 143 | 3.57 | 0 | Hydrophobic |
| C20 | CD1 | PHE- 146 | 4.41 | 0 | Hydrophobic |
| C20 | CD2 | LEU- 147 | 3.55 | 0 | Hydrophobic |
| CL1 | CD1 | TYR- 374 | 3.54 | 0 | Hydrophobic |
