sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
2010-01-05
| Name: | cAMP-dependent protein kinase catalytic subunit alpha |
|---|---|
| ID: | KAPCA_HUMAN |
| AC: | P17612 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.7.11.11 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 92 % |
| D | 8 % |
| B-Factor: | 19.069 |
|---|---|
| Number of residues: | 41 |
| Including | |
| Standard Amino Acids: | 39 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.068 | 563.625 |
| % Hydrophobic | % Polar |
|---|---|
| 55.09 | 44.91 |
| According to VolSite | |
| HET Code: | L9L |
|---|---|
| Formula: | C21H20F3N4OS |
| Molecular weight: | 433.470 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 70.34 % |
| Polar Surface area: | 109.9 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 3 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 75.0813 | 93.7936 | 25.5912 |
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 |
| F1 | CB | LEU- 49 | 3.6 | 0 | Hydrophobic |
| C21 | CD1 | LEU- 49 | 4.28 | 0 | Hydrophobic |
| C12 | CG | PHE- 54 | 3.59 | 0 | Hydrophobic |
| F1 | CB | VAL- 57 | 3.83 | 0 | Hydrophobic |
| S1 | CG2 | VAL- 57 | 3.89 | 0 | Hydrophobic |
| C6 | CG2 | VAL- 57 | 4.31 | 0 | Hydrophobic |
| C4 | CG1 | VAL- 57 | 3.81 | 0 | Hydrophobic |
| C2 | CB | ALA- 70 | 4.1 | 0 | Hydrophobic |
| C21 | CB | ALA- 70 | 3.81 | 0 | Hydrophobic |
| N2 | NZ | LYS- 72 | 2.84 | 151.16 | H-Bond (Protein Donor) |
| C2 | CG1 | VAL- 104 | 3.94 | 0 | Hydrophobic |
| C1 | CG | MET- 120 | 3.83 | 0 | Hydrophobic |
| C2 | CB | MET- 120 | 3.57 | 0 | Hydrophobic |
| N4 | O | GLU- 121 | 2.88 | 150.15 | H-Bond (Ligand Donor) |
| O1 | N | VAL- 123 | 2.76 | 169.99 | H-Bond (Protein Donor) |
| F2 | CG | GLU- 127 | 3.45 | 0 | Hydrophobic |
| C15 | CG | GLU- 127 | 4.38 | 0 | Hydrophobic |
| N3 | OD1 | ASN- 171 | 2.74 | 152.63 | H-Bond (Ligand Donor) |
| F3 | CD2 | LEU- 173 | 3.74 | 0 | Hydrophobic |
| C21 | CD1 | LEU- 173 | 3.77 | 0 | Hydrophobic |
| C6 | CB | THR- 183 | 3.81 | 0 | Hydrophobic |
| C1 | CG2 | THR- 183 | 3.66 | 0 | Hydrophobic |
| C5 | CG2 | THR- 183 | 4.3 | 0 | Hydrophobic |
| N3 | OD2 | ASP- 184 | 2.63 | 175.08 | H-Bond (Ligand Donor) |
| N3 | OD2 | ASP- 184 | 2.63 | 0 | Ionic (Ligand Cationic) |
| F2 | CD1 | PHE- 327 | 3.58 | 0 | Hydrophobic |
| C21 | CE1 | PHE- 327 | 4.48 | 0 | Hydrophobic |
| F3 | CE1 | PHE- 327 | 3.32 | 0 | Hydrophobic |
