sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.900 Å
X-ray
2009-01-23
| 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: | 32.336 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.938 | 702.000 |
| % Hydrophobic | % Polar |
|---|---|
| 44.71 | 55.29 |
| According to VolSite | |
| HET Code: | B98 |
|---|---|
| Formula: | C13H16N3O2S |
| Molecular weight: | 278.350 g/mol |
| DrugBank ID: | DB07431 |
| Buried Surface Area: | 59.68 % |
| Polar Surface area: | 106.24 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| -1.23847 | 28.9012 | 10.0858 |
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 |
| C1 | CD1 | ILE- 10 | 3.83 | 0 | Hydrophobic |
| C18 | CG1 | VAL- 18 | 4.25 | 0 | Hydrophobic |
| C15 | CG2 | VAL- 18 | 3.75 | 0 | Hydrophobic |
| C1 | CB | ALA- 31 | 4.18 | 0 | Hydrophobic |
| C4 | CB | ALA- 31 | 3.47 | 0 | Hydrophobic |
| O10 | NZ | LYS- 33 | 3.04 | 138.53 | H-Bond (Protein Donor) |
| C4 | CG1 | VAL- 64 | 3.95 | 0 | Hydrophobic |
| S7 | CD1 | PHE- 80 | 4.18 | 0 | Hydrophobic |
| C5 | CB | PHE- 80 | 3.6 | 0 | Hydrophobic |
| C1 | CD1 | PHE- 82 | 3.79 | 0 | Hydrophobic |
| O2 | N | LEU- 83 | 3.42 | 175.52 | H-Bond (Protein Donor) |
| N14 | OD1 | ASN- 132 | 2.57 | 164.04 | H-Bond (Ligand Donor) |
| C1 | CD1 | LEU- 134 | 4.22 | 0 | Hydrophobic |
| C3 | CD1 | LEU- 134 | 3.3 | 0 | Hydrophobic |
