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
2006-01-30
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.520 | 8.900 | 8.900 | 0.380 | 9.280 | 2 |
| 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: | 13.636 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.130 | 1225.125 |
| % Hydrophobic | % Polar |
|---|---|
| 42.70 | 57.30 |
| According to VolSite | |
| HET Code: | LIA |
|---|---|
| Formula: | C18H21F2N5O4S |
| Molecular weight: | 441.452 g/mol |
| DrugBank ID: | DB08094 |
| Buried Surface Area: | 64.18 % |
| Polar Surface area: | 135.89 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 1.1567 | 28.45 | 8.53857 |
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 | CG2 | ILE- 10 | 3.9 | 0 | Hydrophobic |
| F24 | CG1 | VAL- 18 | 3.63 | 0 | Hydrophobic |
| F25 | CG2 | VAL- 18 | 3.26 | 0 | Hydrophobic |
| C11 | CB | ALA- 31 | 3.74 | 0 | Hydrophobic |
| C18 | CD | LYS- 33 | 3.95 | 0 | Hydrophobic |
| F24 | CB | LYS- 33 | 3.74 | 0 | Hydrophobic |
| F25 | CB | LYS- 33 | 3.38 | 0 | Hydrophobic |
| F24 | CD2 | PHE- 80 | 3.41 | 0 | Hydrophobic |
| N26 | O | GLU- 81 | 2.74 | 131.6 | H-Bond (Ligand Donor) |
| C3 | CZ | PHE- 82 | 3.92 | 0 | Hydrophobic |
| C4 | CE2 | PHE- 82 | 4.34 | 0 | Hydrophobic |
| N7 | O | LEU- 83 | 2.76 | 122.42 | H-Bond (Ligand Donor) |
| C6 | CB | ASP- 86 | 4.02 | 0 | Hydrophobic |
| O29 | N | ASP- 86 | 3.05 | 151.74 | H-Bond (Protein Donor) |
| C28 | CD | LYS- 89 | 4.43 | 0 | Hydrophobic |
| O30 | NZ | LYS- 89 | 3.21 | 141.37 | H-Bond (Protein Donor) |
| C5 | CD2 | LEU- 134 | 3.78 | 0 | Hydrophobic |
| C11 | CD1 | LEU- 134 | 3.8 | 0 | Hydrophobic |
| C23 | CD2 | LEU- 134 | 4.15 | 0 | Hydrophobic |
| C21 | CB | ALA- 144 | 4.33 | 0 | Hydrophobic |
| C23 | CB | ALA- 144 | 4.06 | 0 | Hydrophobic |
| C20 | CB | ASP- 145 | 3.44 | 0 | Hydrophobic |
