2.500 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: | 59.389 |
---|---|
Number of residues: | 34 |
Including | |
Standard Amino Acids: | 32 |
Non Standard Amino Acids: | 1 |
Water Molecules: | 1 |
Cofactors: | |
Metals: | MG |
Ligandability | Volume (Å3) |
---|---|
0.559 | 550.125 |
% Hydrophobic | % Polar |
---|---|
44.79 | 55.21 |
According to VolSite |
HET Code: | ADP |
---|---|
Formula: | C10H12N5O10P2 |
Molecular weight: | 424.177 g/mol |
DrugBank ID: | - |
Buried Surface Area: | 55.14 % |
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 |
---|---|---|
36.553 | 34.6643 | 65.1881 |
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 |
O1A | ND2 | ASN- 247 | 3.21 | 147.11 | H-Bond (Protein Donor) |
N6 | OD2 | ASP- 282 | 2.79 | 147.42 | H-Bond (Ligand Donor) |
C4' | CD2 | LEU- 295 | 3.76 | 0 | Hydrophobic |
C1' | CD2 | LEU- 295 | 3.64 | 0 | Hydrophobic |
O3B | N | GLY- 317 | 2.85 | 149.89 | H-Bond (Protein Donor) |
O2A | N | LEU- 322 | 3.01 | 176.46 | H-Bond (Protein Donor) |
C5' | CD1 | LEU- 322 | 4.26 | 0 | Hydrophobic |
O2B | MG | MG- 1378 | 2.66 | 0 | Metal Acceptor |
O1A | MG | MG- 1378 | 2.8 | 0 | Metal Acceptor |
N1 | O | HOH- 2101 | 2.8 | 146.31 | H-Bond (Protein Donor) |