sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.850 Å
X-ray
2008-05-20
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.520 | 7.520 | 7.520 | 0.000 | 7.520 | 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: | 28.972 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.214 | 1380.375 |
| % Hydrophobic | % Polar |
|---|---|
| 45.23 | 54.77 |
| According to VolSite | |
| HET Code: | LZE |
|---|---|
| Formula: | C16H18Cl2N5O2 |
| Molecular weight: | 383.252 g/mol |
| DrugBank ID: | DB08142 |
| Buried Surface Area: | 67.33 % |
| Polar Surface area: | 103.48 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 27.4245 | 6.81864 | 63.3348 |
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 |
| C4 | CD1 | ILE- 10 | 4.16 | 0 | Hydrophobic |
| CL7 | CG2 | VAL- 18 | 3.64 | 0 | Hydrophobic |
| C20 | CG2 | VAL- 18 | 3.61 | 0 | Hydrophobic |
| C20 | CD | LYS- 33 | 4.49 | 0 | Hydrophobic |
| CL7 | CD | LYS- 33 | 3.64 | 0 | Hydrophobic |
| CL7 | CE2 | PHE- 80 | 3.72 | 0 | Hydrophobic |
| N11 | O | GLU- 81 | 2.56 | 158.68 | H-Bond (Ligand Donor) |
| C4 | CZ | PHE- 82 | 3.7 | 0 | Hydrophobic |
| N6 | O | LEU- 83 | 2.88 | 140.65 | H-Bond (Ligand Donor) |
| N10 | N | LEU- 83 | 3.02 | 166.97 | H-Bond (Protein Donor) |
| N24 | O | HIS- 84 | 2.8 | 167.66 | H-Bond (Ligand Donor) |
| C25 | CB | ASP- 86 | 4.4 | 0 | Hydrophobic |
| C25 | CD2 | LEU- 134 | 3.83 | 0 | Hydrophobic |
| CL1 | CD2 | LEU- 134 | 3.87 | 0 | Hydrophobic |
| CL1 | CB | ALA- 144 | 3.85 | 0 | Hydrophobic |
| C21 | CB | ASP- 145 | 3.73 | 0 | Hydrophobic |
