sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.400 Å
X-ray
2007-11-28
| Name: | Calcium/calmodulin-dependent protein kinase type II subunit beta |
|---|---|
| ID: | KCC2B_HUMAN |
| AC: | Q13554 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.7.11.17 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 17.169 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.137 | 502.875 |
| % Hydrophobic | % Polar |
|---|---|
| 57.05 | 42.95 |
| According to VolSite | |
| HET Code: | 5CP |
|---|---|
| Formula: | C19H20N8 |
| Molecular weight: | 360.416 g/mol |
| DrugBank ID: | DB07168 |
| Buried Surface Area: | 52.31 % |
| Polar Surface area: | 114.34 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 4 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 34.4847 | 28.4957 | -15.6894 |
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 |
| C1W | CG1 | VAL- 28 | 3.96 | 0 | Hydrophobic |
| C1N | CG2 | VAL- 28 | 3.86 | 0 | Hydrophobic |
| C1V | CG2 | VAL- 28 | 4.33 | 0 | Hydrophobic |
| C1T | CB | ALA- 41 | 4.1 | 0 | Hydrophobic |
| C1T | CG1 | VAL- 74 | 3.82 | 0 | Hydrophobic |
| C1W | CD1 | PHE- 90 | 3.98 | 0 | Hydrophobic |
| C1T | CB | PHE- 90 | 3.76 | 0 | Hydrophobic |
| N1Q | O | ASP- 91 | 2.81 | 143.65 | H-Bond (Ligand Donor) |
| N1P | N | VAL- 93 | 3.23 | 152.08 | H-Bond (Protein Donor) |
| N1G | O | VAL- 93 | 3.11 | 129.11 | H-Bond (Ligand Donor) |
| C1K | CD1 | LEU- 143 | 4.22 | 0 | Hydrophobic |
| C1U | CB | ALA- 156 | 3.79 | 0 | Hydrophobic |
| C1L | CB | ALA- 156 | 4.28 | 0 | Hydrophobic |
| C1L | CB | ASP- 157 | 4.35 | 0 | Hydrophobic |
| C1V | CB | ASP- 157 | 3.56 | 0 | Hydrophobic |
| N1A | O | HOH- 605 | 3.48 | 179.98 | H-Bond (Protein Donor) |
