sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.600 Å
X-ray
2007-06-10
| Name: | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 3, mitochondrial |
|---|---|
| ID: | PDK3_HUMAN |
| AC: | Q15120 |
| 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: | 52.137 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.965 | 435.375 |
| % Hydrophobic | % Polar |
|---|---|
| 47.29 | 52.71 |
| According to VolSite | |
| HET Code: | RDC |
|---|---|
| Formula: | C18H16ClO6 |
| Molecular weight: | 363.769 g/mol |
| DrugBank ID: | DB03758 |
| Buried Surface Area: | 61.42 % |
| Polar Surface area: | 99.19 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 0 |
| X | Y | Z |
|---|---|---|
| -48.7847 | 20.756 | 67.8356 |
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 | CB | ASN- 251 | 4.3 | 0 | Hydrophobic |
| C5 | CB | ASN- 251 | 3.44 | 0 | Hydrophobic |
| C16 | CB | ALA- 255 | 3.76 | 0 | Hydrophobic |
| O3 | OD2 | ASP- 287 | 2.6 | 157.59 | H-Bond (Ligand Donor) |
| O3 | OD1 | ASP- 287 | 3.38 | 134.92 | H-Bond (Ligand Donor) |
| C17 | CG2 | VAL- 292 | 4.4 | 0 | Hydrophobic |
| C18 | CG1 | VAL- 292 | 3.93 | 0 | Hydrophobic |
| C8 | CD1 | LEU- 300 | 3.7 | 0 | Hydrophobic |
| CL1 | CD2 | LEU- 328 | 3.64 | 0 | Hydrophobic |
| C8 | CD1 | LEU- 344 | 4.3 | 0 | Hydrophobic |
| CL1 | CD2 | LEU- 344 | 3.97 | 0 | Hydrophobic |
| C6 | CD2 | LEU- 344 | 4 | 0 | Hydrophobic |
| C2 | CG2 | THR- 352 | 4.15 | 0 | Hydrophobic |
| C3 | CB | THR- 352 | 3.78 | 0 | Hydrophobic |
| C4 | CG2 | THR- 352 | 3.95 | 0 | Hydrophobic |
| O2 | OG1 | THR- 352 | 2.89 | 147.32 | H-Bond (Protein Donor) |
