sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.200 Å
X-ray
2012-12-07
| Name: | cAMP-dependent protein kinase catalytic subunit alpha |
|---|---|
| ID: | KAPCA_MOUSE |
| AC: | P05132 |
| Organism: | Mus musculus |
| Reign: | Eukaryota |
| TaxID: | 10090 |
| EC Number: | 2.7.11.11 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 95 % |
| S | 5 % |
| B-Factor: | 29.365 |
|---|---|
| Number of residues: | 42 |
| Including | |
| Standard Amino Acids: | 38 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.749 | 246.375 |
| % Hydrophobic | % Polar |
|---|---|
| 61.64 | 38.36 |
| According to VolSite | |
| HET Code: | ADP |
|---|---|
| Formula: | C10H12N5O10P2 |
| Molecular weight: | 424.177 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 81.45 % |
| 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 |
|---|---|---|
| -7.53433 | 8.10159 | -13.138 |
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' | CB | LEU- 49 | 4.34 | 0 | Hydrophobic |
| C1' | CB | VAL- 57 | 3.98 | 0 | Hydrophobic |
| C5' | CG2 | VAL- 57 | 3.73 | 0 | Hydrophobic |
| O1B | NZ | LYS- 72 | 3.19 | 0 | Ionic (Protein Cationic) |
| O1A | NZ | LYS- 72 | 2.77 | 0 | Ionic (Protein Cationic) |
| O1A | NZ | LYS- 72 | 2.77 | 167.83 | H-Bond (Protein Donor) |
| N6 | O | GLU- 121 | 2.76 | 154.53 | H-Bond (Ligand Donor) |
| N1 | N | VAL- 123 | 2.99 | 173.5 | H-Bond (Protein Donor) |
| C2' | CG | GLU- 127 | 4.17 | 0 | Hydrophobic |
| O2' | OE2 | GLU- 127 | 2.71 | 166.48 | H-Bond (Ligand Donor) |
| O3' | O | GLU- 170 | 2.99 | 150.77 | H-Bond (Ligand Donor) |
| C2' | CD2 | LEU- 173 | 4.2 | 0 | Hydrophobic |
| N7 | OG1 | THR- 183 | 3.12 | 163 | H-Bond (Protein Donor) |
| C2' | CE1 | PHE- 327 | 4.44 | 0 | Hydrophobic |
| O3' | NH2 | ARG- 618 | 3.07 | 144.1 | H-Bond (Protein Donor) |
| O1A | O | HOH- 1086 | 2.77 | 156.37 | H-Bond (Protein Donor) |
| O1B | O | HOH- 1144 | 2.8 | 137.99 | H-Bond (Protein Donor) |
