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
2008-01-31
| Name: | Calcium/calmodulin-dependent protein kinase type II subunit delta |
|---|---|
| ID: | KCC2D_HUMAN |
| AC: | Q13557 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.7.11.17 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 61.290 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.445 | 1269.000 |
| % Hydrophobic | % Polar |
|---|---|
| 45.48 | 54.52 |
| According to VolSite | |
| HET Code: | GVD |
|---|---|
| Formula: | C22H19N7 |
| Molecular weight: | 381.433 g/mol |
| DrugBank ID: | DB07853 |
| Buried Surface Area: | 53.35 % |
| Polar Surface area: | 102.63 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 2 |
| Rings: | 5 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 12.1909 | 30.8794 | 46.3705 |
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 | CB | LEU- 20 | 3.76 | 0 | Hydrophobic |
| CAJ | CD1 | LEU- 20 | 4.02 | 0 | Hydrophobic |
| CAI | CB | LEU- 20 | 4.19 | 0 | Hydrophobic |
| CAD | CD2 | LEU- 20 | 4.03 | 0 | Hydrophobic |
| CAF | CG2 | VAL- 28 | 3.68 | 0 | Hydrophobic |
| CBB | CB | ALA- 41 | 4.1 | 0 | Hydrophobic |
| NAA | NZ | LYS- 43 | 3.21 | 165.24 | H-Bond (Protein Donor) |
| CBB | CG1 | VAL- 74 | 3.93 | 0 | Hydrophobic |
| CAM | CD1 | PHE- 90 | 4.12 | 0 | Hydrophobic |
| CBB | CB | PHE- 90 | 3.65 | 0 | Hydrophobic |
| NAS | O | ASP- 91 | 2.69 | 165.73 | H-Bond (Ligand Donor) |
| CAJ | CD1 | LEU- 92 | 4.2 | 0 | Hydrophobic |
| NAN | N | VAL- 93 | 3.02 | 154.15 | H-Bond (Protein Donor) |
| NAR | O | VAL- 93 | 3.08 | 132.29 | H-Bond (Ligand Donor) |
| CAG | CD1 | LEU- 143 | 4.26 | 0 | Hydrophobic |
| CAL | CB | ALA- 156 | 4.07 | 0 | Hydrophobic |
| CA0 | CB | ASP- 157 | 4.21 | 0 | Hydrophobic |
