sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.550 Å
X-ray
2012-06-13
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.000 | 7.000 | 7.000 | 0.000 | 7.000 | 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: | 29.612 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.925 | 560.250 |
| % Hydrophobic | % Polar |
|---|---|
| 49.40 | 50.60 |
| According to VolSite | |
| HET Code: | 20K |
|---|---|
| Formula: | C17H18ClN5S |
| Molecular weight: | 359.876 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 57.77 % |
| Polar Surface area: | 82.18 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| -2.19704 | -6.88392 | 27.1213 |
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 |
| C16 | CG2 | ILE- 10 | 4.38 | 0 | Hydrophobic |
| C12 | CB | ILE- 10 | 4.16 | 0 | Hydrophobic |
| C10 | CD1 | ILE- 10 | 3.72 | 0 | Hydrophobic |
| S | CG1 | VAL- 18 | 4.5 | 0 | Hydrophobic |
| C1 | CG2 | VAL- 18 | 4.32 | 0 | Hydrophobic |
| C4 | CG1 | VAL- 18 | 4.32 | 0 | Hydrophobic |
| C7 | CB | ALA- 31 | 3.53 | 0 | Hydrophobic |
| C7 | CG1 | VAL- 64 | 4.26 | 0 | Hydrophobic |
| C4 | CD2 | PHE- 80 | 3.69 | 0 | Hydrophobic |
| C7 | CB | PHE- 80 | 4.43 | 0 | Hydrophobic |
| CL | CZ | PHE- 82 | 4.4 | 0 | Hydrophobic |
| N2 | N | LEU- 83 | 2.99 | 171.87 | H-Bond (Protein Donor) |
| N3 | O | LEU- 83 | 2.88 | 152.76 | H-Bond (Ligand Donor) |
| C15 | CG | GLN- 85 | 4.43 | 0 | Hydrophobic |
| C12 | CB | ASP- 86 | 4.11 | 0 | Hydrophobic |
| C15 | CD | LYS- 89 | 3.5 | 0 | Hydrophobic |
| C7 | CG | LEU- 134 | 4.15 | 0 | Hydrophobic |
| C11 | CD1 | LEU- 134 | 3.6 | 0 | Hydrophobic |
| C4 | CB | ALA- 144 | 4.32 | 0 | Hydrophobic |
| C4 | CB | ASP- 145 | 4.19 | 0 | Hydrophobic |
