sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.260 Å
X-ray
2012-06-13
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 5.190 | 5.190 | 5.190 | 0.000 | 5.190 | 1 |
| Name: | Cyclin-dependent kinase 2 |
|---|---|
| ID: | CDK2_HUMAN |
| AC: | P24941 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.7.11.22 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 16.280 |
|---|---|
| Number of residues: | 26 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.355 | 725.625 |
| % Hydrophobic | % Polar |
|---|---|
| 37.21 | 62.79 |
| According to VolSite | |
| HET Code: | CK2 |
|---|---|
| Formula: | C9H10N4S |
| Molecular weight: | 206.268 g/mol |
| DrugBank ID: | DB02091 |
| Buried Surface Area: | 66.06 % |
| Polar Surface area: | 92.93 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 1 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 1 |
| X | Y | Z |
|---|---|---|
| 0.288429 | 7.41186 | 27.3994 |
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 |
| S4A | CG1 | ILE- 10 | 4.3 | 0 | Hydrophobic |
| C5 | CD1 | ILE- 10 | 3.69 | 0 | Hydrophobic |
| C7A | CG2 | VAL- 18 | 4.44 | 0 | Hydrophobic |
| S4A | CG1 | VAL- 18 | 3.94 | 0 | Hydrophobic |
| N3 | NZ | LYS- 33 | 3.22 | 149.08 | H-Bond (Protein Donor) |
| DuAr | NZ | LYS- 33 | 3.95 | 138.35 | Pi/Cation |
| N7 | O | GLU- 81 | 2.92 | 169.33 | H-Bond (Ligand Donor) |
| N1 | N | LEU- 83 | 3.41 | 172.1 | H-Bond (Protein Donor) |
| C6A | CB | ASN- 132 | 4.35 | 0 | Hydrophobic |
| C6A | CD1 | LEU- 134 | 4.37 | 0 | Hydrophobic |
| C5 | CD1 | LEU- 134 | 4.14 | 0 | Hydrophobic |
| C6A | CB | ALA- 144 | 3.7 | 0 | Hydrophobic |
