sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.900 Å
X-ray
2010-08-10
| Name: | cGMP-dependent protein kinase 1 |
|---|---|
| ID: | KGP1_HUMAN |
| AC: | Q13976 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.7.11.12 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 20 % |
| B | 80 % |
| B-Factor: | 71.907 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.676 | 519.750 |
| % Hydrophobic | % Polar |
|---|---|
| 41.56 | 58.44 |
| According to VolSite | |
| HET Code: | PCG |
|---|---|
| Formula: | C10H11N5O7P |
| Molecular weight: | 344.197 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 79.29 % |
| Polar Surface area: | 183.16 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 10 |
| H-Bond Donors: | 3 |
| Rings: | 4 |
| Aromatic rings: | 1 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 1 |
| X | Y | Z |
|---|---|---|
| 0.914087 | -22.028 | 17.9033 |
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 |
| C5' | CG2 | ILE- 146 | 4.37 | 0 | Hydrophobic |
| C1' | CE | MET- 175 | 4.28 | 0 | Hydrophobic |
| C1' | CB | PHE- 181 | 4.03 | 0 | Hydrophobic |
| O1A | O | GLY- 182 | 3.33 | 126.56 | H-Bond (Ligand Donor) |
| O2' | N | GLY- 182 | 3.03 | 141.69 | H-Bond (Protein Donor) |
| O3' | N | LEU- 184 | 3.38 | 143.49 | H-Bond (Protein Donor) |
| C3' | CD2 | LEU- 184 | 3.64 | 0 | Hydrophobic |
| O1A | N | ALA- 185 | 3.15 | 157.24 | H-Bond (Protein Donor) |
| N1 | O | LEU- 187 | 2.85 | 156.02 | H-Bond (Ligand Donor) |
| N2 | O | LEU- 187 | 3.12 | 138.65 | H-Bond (Ligand Donor) |
| O1A | NH1 | ARG- 192 | 2.8 | 151.57 | H-Bond (Protein Donor) |
| O2A | N | THR- 193 | 2.82 | 162.37 | H-Bond (Protein Donor) |
| O2A | OG1 | THR- 193 | 2.72 | 169.39 | H-Bond (Protein Donor) |
| N2 | OG1 | THR- 193 | 2.68 | 155.34 | H-Bond (Ligand Donor) |
| C5' | CB | ALA- 194 | 3.97 | 0 | Hydrophobic |
| C5' | CG2 | VAL- 196 | 3.92 | 0 | Hydrophobic |
