sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.530 Å
X-ray
2003-07-04
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.220 | 7.220 | 7.220 | 0.000 | 7.220 | 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: | 40.617 |
|---|---|
| Number of residues: | 24 |
| Including | |
| Standard Amino Acids: | 24 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.945 | 857.250 |
| % Hydrophobic | % Polar |
|---|---|
| 46.85 | 53.15 |
| According to VolSite | |
| HET Code: | CK5 |
|---|---|
| Formula: | C15H14N4OS |
| Molecular weight: | 298.363 g/mol |
| DrugBank ID: | DB04518 |
| Buried Surface Area: | 63.47 % |
| Polar Surface area: | 99.17 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 14.8857 | 44.7034 | 12.051 |
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 | CG2 | ILE- 10 | 3.99 | 0 | Hydrophobic |
| C2B | CG2 | ILE- 10 | 3.39 | 0 | Hydrophobic |
| C1B | CD1 | ILE- 10 | 3.84 | 0 | Hydrophobic |
| C7A | CG2 | VAL- 18 | 4.45 | 0 | Hydrophobic |
| C5 | CB | ALA- 31 | 3.63 | 0 | Hydrophobic |
| C5 | CG1 | VAL- 64 | 3.97 | 0 | Hydrophobic |
| C5 | CB | PHE- 80 | 4.28 | 0 | Hydrophobic |
| C6A | CD2 | PHE- 80 | 3.43 | 0 | Hydrophobic |
| N7 | O | LEU- 83 | 2.81 | 138.38 | H-Bond (Ligand Donor) |
| N1 | N | LEU- 83 | 3.08 | 158.68 | H-Bond (Protein Donor) |
| O7B | OD2 | ASP- 86 | 2.72 | 120.36 | H-Bond (Ligand Donor) |
| C3B | CB | ASP- 86 | 3.69 | 0 | Hydrophobic |
| C7A | CB | ASN- 132 | 4.43 | 0 | Hydrophobic |
| C5 | CD1 | LEU- 134 | 3.41 | 0 | Hydrophobic |
| S4A | CD2 | LEU- 134 | 4.11 | 0 | Hydrophobic |
| C2B | CD2 | LEU- 134 | 3.52 | 0 | Hydrophobic |
| C6A | CB | ALA- 144 | 4.1 | 0 | Hydrophobic |
