sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.600 Å
X-ray
2003-05-13
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 5.620 | 5.620 | 5.620 | 0.000 | 5.620 | 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 |
|---|---|
| C | 100 % |
| B-Factor: | 32.992 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.997 | 502.875 |
| % Hydrophobic | % Polar |
|---|---|
| 52.35 | 47.65 |
| According to VolSite | |
| HET Code: | ST8 |
|---|---|
| Formula: | C18H22N6O3 |
| Molecular weight: | 370.406 g/mol |
| DrugBank ID: | DB08572 |
| Buried Surface Area: | 60.01 % |
| Polar Surface area: | 145.57 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 33.8825 | 85.1868 | 43.019 |
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 |
| C10 | CG2 | ILE- 10 | 3.4 | 0 | Hydrophobic |
| C22 | CG2 | ILE- 10 | 3.95 | 0 | Hydrophobic |
| C18 | CD1 | ILE- 10 | 4.02 | 0 | Hydrophobic |
| C10 | CG1 | VAL- 18 | 4.2 | 0 | Hydrophobic |
| C11 | CG2 | VAL- 18 | 4.46 | 0 | Hydrophobic |
| N9 | O | GLU- 81 | 2.97 | 148.86 | H-Bond (Ligand Donor) |
| N2 | O | LEU- 83 | 2.69 | 144.18 | H-Bond (Ligand Donor) |
| C19 | CB | GLN- 85 | 4.28 | 0 | Hydrophobic |
| C21 | CB | ASP- 86 | 4.5 | 0 | Hydrophobic |
| N25 | OD2 | ASP- 86 | 2.6 | 158.66 | H-Bond (Ligand Donor) |
| C22 | CD2 | LEU- 134 | 4.1 | 0 | Hydrophobic |
| C13 | CB | ASP- 145 | 4.49 | 0 | Hydrophobic |
