sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
2007-11-16
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.620 | 7.620 | 7.620 | 0.000 | 7.620 | 1 |
| Name: | Casein kinase II subunit alpha |
|---|---|
| ID: | CSK2A_MAIZE |
| AC: | P28523 |
| Organism: | Zea mays |
| Reign: | Eukaryota |
| TaxID: | 4577 |
| EC Number: | 2.7.11.1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 22.339 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 29 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.023 | 891.000 |
| % Hydrophobic | % Polar |
|---|---|
| 53.41 | 46.59 |
| According to VolSite | |
| HET Code: | P04 |
|---|---|
| Formula: | C19H21N7O |
| Molecular weight: | 363.416 g/mol |
| DrugBank ID: | DB08338 |
| Buried Surface Area: | 66.76 % |
| Polar Surface area: | 96.24 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 3 |
| Rings: | 5 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| 22.6326 | 7.04952 | 19.6227 |
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 |
| C12 | CB | VAL- 45 | 3.77 | 0 | Hydrophobic |
| C18 | CG1 | VAL- 53 | 3.77 | 0 | Hydrophobic |
| C19 | CG2 | VAL- 53 | 3.83 | 0 | Hydrophobic |
| C21 | CG2 | VAL- 53 | 3.49 | 0 | Hydrophobic |
| C12 | CD1 | ILE- 66 | 4.47 | 0 | Hydrophobic |
| C33 | CB | ILE- 66 | 4.36 | 0 | Hydrophobic |
| C32 | CG2 | ILE- 66 | 3.5 | 0 | Hydrophobic |
| O29 | NZ | LYS- 68 | 3.01 | 160.34 | H-Bond (Protein Donor) |
| C30 | CD | LYS- 68 | 3.96 | 0 | Hydrophobic |
| C33 | CG2 | VAL- 95 | 3.55 | 0 | Hydrophobic |
| C30 | CE2 | PHE- 113 | 4.14 | 0 | Hydrophobic |
| C33 | CB | PHE- 113 | 3.93 | 0 | Hydrophobic |
| C32 | CD2 | PHE- 113 | 3.6 | 0 | Hydrophobic |
| C12 | CE1 | TYR- 115 | 4.1 | 0 | Hydrophobic |
| C13 | CZ | TYR- 115 | 3.98 | 0 | Hydrophobic |
| N01 | N | VAL- 116 | 3.03 | 137.68 | H-Bond (Protein Donor) |
| N10 | O | VAL- 116 | 2.88 | 149.2 | H-Bond (Ligand Donor) |
| C11 | CB | ASN- 118 | 3.89 | 0 | Hydrophobic |
| C11 | SD | MET- 163 | 4.45 | 0 | Hydrophobic |
| C31 | CD1 | ILE- 174 | 3.77 | 0 | Hydrophobic |
| C33 | CG2 | ILE- 174 | 3.82 | 0 | Hydrophobic |
| C19 | CD1 | ILE- 174 | 3.67 | 0 | Hydrophobic |
| N27 | OD1 | ASP- 175 | 3.05 | 168.97 | H-Bond (Ligand Donor) |
