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
2011-03-25
| 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: | 35.939 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.980 | 526.500 |
| % Hydrophobic | % Polar |
|---|---|
| 51.92 | 48.08 |
| According to VolSite | |
| HET Code: | Z71 |
|---|---|
| Formula: | C16H13F2N5O3S2 |
| Molecular weight: | 425.433 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 63.51 % |
| Polar Surface area: | 176.82 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| -66.0833 | -80.414 | -11.8536 |
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 |
| S5 | CD1 | ILE- 10 | 3.54 | 0 | Hydrophobic |
| C13 | CD1 | ILE- 10 | 4.01 | 0 | Hydrophobic |
| F28 | CG | LYS- 33 | 3.36 | 0 | Hydrophobic |
| F28 | CE2 | PHE- 80 | 3.3 | 0 | Hydrophobic |
| N3 | N | LEU- 83 | 3.11 | 176.74 | H-Bond (Protein Donor) |
| N8 | O | LEU- 83 | 2.73 | 149.12 | H-Bond (Ligand Donor) |
| O17 | N | ASP- 86 | 3.14 | 165.65 | H-Bond (Protein Donor) |
| N18 | OD2 | ASP- 86 | 3.15 | 148.42 | H-Bond (Ligand Donor) |
| C15 | CB | ASP- 86 | 3.9 | 0 | Hydrophobic |
| S5 | CD1 | LEU- 134 | 3.73 | 0 | Hydrophobic |
| C14 | CD2 | LEU- 134 | 3.95 | 0 | Hydrophobic |
| C23 | CB | ASP- 145 | 3.85 | 0 | Hydrophobic |
| F27 | CB | ASP- 145 | 3.3 | 0 | Hydrophobic |
| C21 | CB | ASP- 145 | 3.21 | 0 | Hydrophobic |
| O19 | O | HOH- 350 | 3.47 | 159.88 | H-Bond (Protein Donor) |
