sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.900 Å
X-ray
2012-12-06
| 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: | 23.789 |
|---|---|
| Number of residues: | 43 |
| Including | |
| Standard Amino Acids: | 38 |
| Non Standard Amino Acids: | 3 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | MG MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.481 | 243.000 |
| % Hydrophobic | % Polar |
|---|---|
| 63.89 | 36.11 |
| According to VolSite | |
| HET Code: | ADP |
|---|---|
| Formula: | C10H12N5O10P2 |
| Molecular weight: | 424.177 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 82.1 % |
| 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 |
|---|---|---|
| -7.71307 | 8.34363 | -13.414 |
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 | VAL- 57 | 4.1 | 0 | Hydrophobic |
| C5' | CG2 | VAL- 57 | 3.67 | 0 | Hydrophobic |
| O1B | NZ | LYS- 72 | 2.92 | 140.07 | H-Bond (Protein Donor) |
| O1A | NZ | LYS- 72 | 3.08 | 173.55 | H-Bond (Protein Donor) |
| O1B | NZ | LYS- 72 | 2.92 | 0 | Ionic (Protein Cationic) |
| O1A | NZ | LYS- 72 | 3.08 | 0 | Ionic (Protein Cationic) |
| N6 | O | GLU- 121 | 2.77 | 152.79 | H-Bond (Ligand Donor) |
| N1 | N | VAL- 123 | 3.06 | 175.21 | H-Bond (Protein Donor) |
| C2' | CG | GLU- 127 | 4.08 | 0 | Hydrophobic |
| O2' | OE2 | GLU- 127 | 2.59 | 142.09 | H-Bond (Ligand Donor) |
| O3' | O | GLU- 170 | 2.74 | 155.51 | H-Bond (Ligand Donor) |
| C2' | CD2 | LEU- 173 | 4.12 | 0 | Hydrophobic |
| N7 | OG1 | THR- 183 | 3.22 | 174.14 | H-Bond (Protein Donor) |
| O1B | MG | MG- 401 | 2.03 | 0 | Metal Acceptor |
| O3B | MG | MG- 402 | 1.99 | 0 | Metal Acceptor |
| O2A | MG | MG- 402 | 1.97 | 0 | Metal Acceptor |
| O3' | NH2 | ARG- 618 | 3.04 | 129.99 | H-Bond (Protein Donor) |
