sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
1997-08-05
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.090 | 8.140 | 8.160 | 0.030 | 8.160 | 3 |
| 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: | 25.205 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.029 | 857.250 |
| % Hydrophobic | % Polar |
|---|---|
| 46.46 | 53.54 |
| According to VolSite | |
| HET Code: | STU |
|---|---|
| Formula: | C28H27N4O3 |
| Molecular weight: | 467.539 g/mol |
| DrugBank ID: | DB02010 |
| Buried Surface Area: | 66.99 % |
| Polar Surface area: | 74.03 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 2 |
| Rings: | 8 |
| Aromatic rings: | 5 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| 0.5166 | 27.0616 | 8.97183 |
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 |
| C6 | CD1 | ILE- 10 | 3.89 | 0 | Hydrophobic |
| C1 | CB | ILE- 10 | 4.3 | 0 | Hydrophobic |
| C5 | CD1 | ILE- 10 | 3.71 | 0 | Hydrophobic |
| C26 | CG2 | VAL- 18 | 4.14 | 0 | Hydrophobic |
| C18 | CG1 | VAL- 18 | 4.19 | 0 | Hydrophobic |
| C17 | CG2 | VAL- 18 | 3.78 | 0 | Hydrophobic |
| C7 | CB | ALA- 31 | 3.96 | 0 | Hydrophobic |
| C15 | CD | LYS- 33 | 3.93 | 0 | Hydrophobic |
| N1 | O | GLU- 81 | 2.75 | 163.27 | H-Bond (Ligand Donor) |
| O5 | N | LEU- 83 | 2.63 | 165.93 | H-Bond (Protein Donor) |
| C24 | CB | ASP- 86 | 4.43 | 0 | Hydrophobic |
| N4 | OD2 | ASP- 86 | 2.82 | 153.8 | H-Bond (Ligand Donor) |
| N4 | OD2 | ASP- 86 | 2.82 | 0 | Ionic (Ligand Cationic) |
| N4 | O | GLN- 131 | 2.86 | 141.47 | H-Bond (Ligand Donor) |
| C27 | CB | ASN- 132 | 4.36 | 0 | Hydrophobic |
| C27 | CD2 | LEU- 134 | 3.87 | 0 | Hydrophobic |
| C6 | CD2 | LEU- 134 | 3.68 | 0 | Hydrophobic |
| C10 | CD1 | LEU- 134 | 3.53 | 0 | Hydrophobic |
| C6 | CD2 | LEU- 134 | 3.68 | 0 | Hydrophobic |
| C27 | CB | ALA- 144 | 4.06 | 0 | Hydrophobic |
| C15 | CB | ASP- 145 | 3.5 | 0 | Hydrophobic |
