sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.820 Å
X-ray
2014-05-29
| Name: | Circadian clock protein kinase KaiC |
|---|---|
| ID: | KAIC_SYNE7 |
| AC: | Q79PF4 |
| Organism: | Synechococcus elongatus |
| Reign: | Bacteria |
| TaxID: | 1140 |
| EC Number: | 2.7.11.1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 38 % |
| F | 62 % |
| B-Factor: | 25.591 |
|---|---|
| Number of residues: | 43 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 5 |
| Cofactors: | |
| Metals: | CL MG |
| Ligandability | Volume (Å3) |
|---|---|
| 1.132 | 1431.000 |
| % Hydrophobic | % Polar |
|---|---|
| 45.52 | 54.48 |
| According to VolSite | |
| HET Code: | AGS |
|---|---|
| Formula: | C10H14N5O12P3S |
| Molecular weight: | 521.231 g/mol |
| DrugBank ID: | DB02930 |
| Buried Surface Area: | 74.94 % |
| Polar Surface area: | 329.24 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 17 |
| H-Bond Donors: | 5 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| -39.6948 | 4.31416 | 7.95174 |
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 |
| O3B | N | GLY- 49 | 3.03 | 142.44 | H-Bond (Protein Donor) |
| O2B | N | THR- 50 | 3.11 | 125.29 | H-Bond (Protein Donor) |
| O2B | N | GLY- 51 | 3.16 | 139.84 | H-Bond (Protein Donor) |
| O3A | N | GLY- 51 | 3.39 | 142.9 | H-Bond (Protein Donor) |
| O2B | N | LYS- 52 | 3.07 | 156.93 | H-Bond (Protein Donor) |
| O2B | NZ | LYS- 52 | 2.82 | 161.73 | H-Bond (Protein Donor) |
| O2B | NZ | LYS- 52 | 2.82 | 0 | Ionic (Protein Cationic) |
| O1B | N | THR- 53 | 3.04 | 159.07 | H-Bond (Protein Donor) |
| O1A | N | LEU- 54 | 2.79 | 155.45 | H-Bond (Protein Donor) |
| N6 | OG | SER- 89 | 3.4 | 172.61 | H-Bond (Ligand Donor) |
| O3G | NZ | LYS- 224 | 2.56 | 140.68 | H-Bond (Protein Donor) |
| O3G | NZ | LYS- 224 | 2.56 | 0 | Ionic (Protein Cationic) |
| C3' | CG | LYS- 224 | 4.44 | 0 | Hydrophobic |
| O3' | N | LEU- 225 | 3.09 | 144.41 | H-Bond (Protein Donor) |
| O3G | NH2 | ARG- 226 | 2.93 | 136.12 | H-Bond (Protein Donor) |
| O3G | NE | ARG- 226 | 3.05 | 134.79 | H-Bond (Protein Donor) |
| O3G | CZ | ARG- 226 | 3.38 | 0 | Ionic (Protein Cationic) |
| O2' | NE2 | HIS- 230 | 2.74 | 170.42 | H-Bond (Ligand Donor) |
| C4' | CD1 | ILE- 239 | 4.42 | 0 | Hydrophobic |
| C1' | CG2 | ILE- 239 | 3.94 | 0 | Hydrophobic |
| N6 | OD1 | ASP- 241 | 3.12 | 169.16 | H-Bond (Ligand Donor) |
| O2G | MG | MG- 301 | 1.86 | 0 | Metal Acceptor |
| O1B | MG | MG- 301 | 2 | 0 | Metal Acceptor |
| O3' | O | HOH- 429 | 2.78 | 155.64 | H-Bond (Ligand Donor) |
| N3 | O | HOH- 475 | 2.84 | 179.95 | H-Bond (Protein Donor) |
