sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.500 Å
X-ray
2006-11-13
| 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: | 19.089 |
|---|---|
| Number of residues: | 24 |
| Including | |
| Standard Amino Acids: | 24 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.090 | 1140.750 |
| % Hydrophobic | % Polar |
|---|---|
| 45.56 | 54.44 |
| According to VolSite | |
| HET Code: | PY8 |
|---|---|
| Formula: | C13H14BrN5O2S |
| Molecular weight: | 384.252 g/mol |
| DrugBank ID: | DB08441 |
| Buried Surface Area: | 62.33 % |
| Polar Surface area: | 104.38 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 0 |
| X | Y | Z |
|---|---|---|
| 3.10423 | 27.5019 | 7.08782 |
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 |
| C9 | CG1 | ILE- 10 | 4.47 | 0 | Hydrophobic |
| C17 | CG2 | ILE- 10 | 4.46 | 0 | Hydrophobic |
| C19 | CD1 | ILE- 10 | 4.05 | 0 | Hydrophobic |
| N13 | O | ILE- 10 | 3.1 | 153.74 | H-Bond (Ligand Donor) |
| C1 | CB | ALA- 31 | 3.53 | 0 | Hydrophobic |
| BR1 | CB | PHE- 80 | 3.89 | 0 | Hydrophobic |
| C18 | CZ | PHE- 82 | 3.08 | 0 | Hydrophobic |
| N3 | N | LEU- 83 | 2.9 | 175 | H-Bond (Protein Donor) |
| C10 | CB | ASP- 86 | 3.91 | 0 | Hydrophobic |
| O15 | N | ASP- 86 | 2.74 | 130.63 | H-Bond (Protein Donor) |
| C8 | CD2 | LEU- 134 | 4.14 | 0 | Hydrophobic |
| C10 | CD2 | LEU- 134 | 4.1 | 0 | Hydrophobic |
| C20 | CD2 | LEU- 134 | 4.1 | 0 | Hydrophobic |
| C1 | CD1 | LEU- 134 | 3.55 | 0 | Hydrophobic |
