sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
2004-03-29
| 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 | 95 % |
| B | 5 % |
| B-Factor: | 34.746 |
|---|---|
| Number of residues: | 46 |
| Including | |
| Standard Amino Acids: | 42 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 4 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.837 | 722.250 |
| % Hydrophobic | % Polar |
|---|---|
| 46.73 | 53.27 |
| According to VolSite | |
| HET Code: | I08 |
|---|---|
| Formula: | C28H29FN3O4 |
| Molecular weight: | 490.546 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 75.22 % |
| Polar Surface area: | 105.13 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| 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 |
|---|---|---|
| 30.5003 | 19.6938 | 8.83486 |
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 |
| C15 | CD1 | LEU- 49 | 4.4 | 0 | Hydrophobic |
| F96 | CB | SER- 53 | 3.25 | 0 | Hydrophobic |
| F96 | CE2 | PHE- 54 | 3.49 | 0 | Hydrophobic |
| C98 | CE2 | PHE- 54 | 4.28 | 0 | Hydrophobic |
| O62 | N | PHE- 54 | 2.96 | 150.55 | H-Bond (Protein Donor) |
| C37 | CG2 | VAL- 57 | 4.16 | 0 | Hydrophobic |
| C51 | CG2 | VAL- 57 | 4.13 | 0 | Hydrophobic |
| C14 | CG1 | VAL- 57 | 4.05 | 0 | Hydrophobic |
| C13 | CB | ALA- 70 | 3.85 | 0 | Hydrophobic |
| C52 | CG | LYS- 72 | 4.48 | 0 | Hydrophobic |
| C53 | CD | LYS- 72 | 4.44 | 0 | Hydrophobic |
| DuAr | NZ | LYS- 72 | 3.89 | 28.81 | Pi/Cation |
| C72 | CD1 | LEU- 74 | 4.09 | 0 | Hydrophobic |
| C71 | CD2 | LEU- 74 | 4.38 | 0 | Hydrophobic |
| C53 | CD2 | LEU- 74 | 3.7 | 0 | Hydrophobic |
| C98 | CG | GLN- 84 | 4.11 | 0 | Hydrophobic |
| C98 | CB | HIS- 87 | 3.9 | 0 | Hydrophobic |
| C74 | CB | HIS- 87 | 4.42 | 0 | Hydrophobic |
| C73 | CG2 | THR- 88 | 4.23 | 0 | Hydrophobic |
| O92 | OE1 | GLU- 91 | 2.61 | 157.17 | H-Bond (Ligand Donor) |
| C13 | SD | MET- 120 | 4.28 | 0 | Hydrophobic |
| N11 | N | VAL- 123 | 3.08 | 159.88 | H-Bond (Protein Donor) |
| N33 | OE2 | GLU- 127 | 4 | 0 | Ionic (Ligand Cationic) |
| N33 | O | GLU- 170 | 2.94 | 128.99 | H-Bond (Ligand Donor) |
| N33 | OD1 | ASN- 171 | 3.12 | 126.31 | H-Bond (Ligand Donor) |
| C14 | CG | LEU- 173 | 4.33 | 0 | Hydrophobic |
| C15 | CD1 | LEU- 173 | 3.72 | 0 | Hydrophobic |
| C13 | CG2 | THR- 183 | 3.78 | 0 | Hydrophobic |
| N33 | OD2 | ASP- 184 | 2.94 | 121.62 | H-Bond (Ligand Donor) |
| N33 | OD1 | ASP- 184 | 3.5 | 166.53 | H-Bond (Ligand Donor) |
| N33 | OD2 | ASP- 184 | 2.94 | 0 | Ionic (Ligand Cationic) |
| N33 | OD1 | ASP- 184 | 3.5 | 0 | Ionic (Ligand Cationic) |
| C98 | CZ | PHE- 187 | 3.76 | 0 | Hydrophobic |
| N23 | O | HOH- 364 | 3.11 | 166.7 | H-Bond (Ligand Donor) |
| O22 | O | HOH- 379 | 3.14 | 179.96 | H-Bond (Protein Donor) |
