sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.700 Å
X-ray
2011-07-13
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.160 | 6.160 | 6.160 | 0.000 | 6.160 | 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 |
|---|---|
| A | 100 % |
| B-Factor: | 27.900 |
|---|---|
| Number of residues: | 26 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.832 | 573.750 |
| % Hydrophobic | % Polar |
|---|---|
| 47.65 | 52.35 |
| According to VolSite | |
| HET Code: | 18K |
|---|---|
| Formula: | C16H18N6S |
| Molecular weight: | 326.419 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 61.84 % |
| Polar Surface area: | 108.19 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 11.4769 | 9.16035 | -11.3524 |
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 |
| S | CD1 | ILE- 10 | 4.49 | 0 | Hydrophobic |
| C11 | CG2 | ILE- 10 | 4.39 | 0 | Hydrophobic |
| C15 | CB | ILE- 10 | 4.03 | 0 | Hydrophobic |
| C9 | CD1 | ILE- 10 | 3.79 | 0 | Hydrophobic |
| S | CG1 | VAL- 18 | 4.18 | 0 | Hydrophobic |
| C6 | CB | ALA- 31 | 3.47 | 0 | Hydrophobic |
| C6 | CG1 | VAL- 64 | 4.2 | 0 | Hydrophobic |
| C1 | CD2 | PHE- 80 | 3.66 | 0 | Hydrophobic |
| C6 | CB | PHE- 80 | 4.43 | 0 | Hydrophobic |
| N3 | N | LEU- 83 | 2.94 | 170.21 | H-Bond (Protein Donor) |
| N4 | O | LEU- 83 | 2.88 | 160.14 | H-Bond (Ligand Donor) |
| C13 | CG | GLN- 85 | 4.42 | 0 | Hydrophobic |
| C15 | CB | ASP- 86 | 4.27 | 0 | Hydrophobic |
| C13 | CD | LYS- 89 | 3.65 | 0 | Hydrophobic |
| C6 | CG | LEU- 134 | 4.25 | 0 | Hydrophobic |
| C16 | CD1 | LEU- 134 | 3.68 | 0 | Hydrophobic |
| C1 | CB | ALA- 144 | 3.98 | 0 | Hydrophobic |
