sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.800 Å
X-ray
2009-11-06
| Name: | cAMP-dependent protein kinase catalytic subunit alpha |
|---|---|
| ID: | KAPCA_BOVIN |
| AC: | P00517 |
| Organism: | Bos taurus |
| Reign: | Eukaryota |
| TaxID: | 9913 |
| EC Number: | 2.7.11.11 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 30.967 |
|---|---|
| Number of residues: | 40 |
| Including | |
| Standard Amino Acids: | 39 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.850 | 776.250 |
| % Hydrophobic | % Polar |
|---|---|
| 47.39 | 52.61 |
| According to VolSite | |
| HET Code: | B99 |
|---|---|
| Formula: | C28H26N5O2 |
| Molecular weight: | 464.538 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 64.03 % |
| Polar Surface area: | 107.37 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 3 |
| Rings: | 6 |
| Aromatic rings: | 6 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| -26.9011 | -10.6395 | -0.987057 |
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 |
| C1 | CD1 | LEU- 49 | 3.87 | 0 | Hydrophobic |
| C7 | CG1 | VAL- 57 | 4.15 | 0 | Hydrophobic |
| C9 | CG2 | VAL- 57 | 4.19 | 0 | Hydrophobic |
| C20 | CG2 | VAL- 57 | 3.57 | 0 | Hydrophobic |
| C1 | CB | ALA- 70 | 4.32 | 0 | Hydrophobic |
| C3 | CB | ALA- 70 | 3.6 | 0 | Hydrophobic |
| N5 | NZ | LYS- 72 | 2.86 | 150.67 | H-Bond (Protein Donor) |
| C19 | CD | LYS- 72 | 3.64 | 0 | Hydrophobic |
| C4 | CG1 | VAL- 104 | 3.68 | 0 | Hydrophobic |
| C4 | CB | MET- 120 | 4.03 | 0 | Hydrophobic |
| C5 | SD | MET- 120 | 4.04 | 0 | Hydrophobic |
| N2 | O | GLU- 121 | 2.76 | 152.54 | H-Bond (Ligand Donor) |
| C1 | CE1 | TYR- 122 | 4.43 | 0 | Hydrophobic |
| N1 | N | VAL- 123 | 3.42 | 153.35 | H-Bond (Protein Donor) |
| N3 | OD1 | ASN- 171 | 2.51 | 167.79 | H-Bond (Ligand Donor) |
| C1 | CD1 | LEU- 173 | 4.01 | 0 | Hydrophobic |
| C8 | CD1 | LEU- 173 | 3.64 | 0 | Hydrophobic |
| C5 | CG2 | THR- 183 | 3.68 | 0 | Hydrophobic |
| C10 | CB | THR- 183 | 3.65 | 0 | Hydrophobic |
| C12 | CB | ASP- 184 | 4.47 | 0 | Hydrophobic |
| C11 | CB | ASP- 184 | 3.53 | 0 | Hydrophobic |
| N3 | OD2 | ASP- 184 | 3.01 | 131.05 | H-Bond (Ligand Donor) |
| N3 | OD2 | ASP- 184 | 3.01 | 0 | Ionic (Ligand Cationic) |
| C1 | CE1 | PHE- 327 | 3.63 | 0 | Hydrophobic |
