sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.400 Å
X-ray
2005-06-29
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 5.470 | 5.500 | 5.500 | 0.040 | 5.540 | 2 |
| 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: | 21.675 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.689 | 675.000 |
| % Hydrophobic | % Polar |
|---|---|
| 41.50 | 58.50 |
| According to VolSite | |
| HET Code: | RRC |
|---|---|
| Formula: | C19H26N6O |
| Molecular weight: | 354.449 g/mol |
| DrugBank ID: | DB06195 |
| Buried Surface Area: | 59.96 % |
| Polar Surface area: | 87.89 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 100.865 | 101.747 | 79.8926 |
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 |
| CAE | CG2 | ILE- 10 | 3.79 | 0 | Hydrophobic |
| CAH | CG1 | ILE- 10 | 4.37 | 0 | Hydrophobic |
| CAB | CG2 | ILE- 10 | 3.62 | 0 | Hydrophobic |
| CBA | CG1 | VAL- 18 | 3.53 | 0 | Hydrophobic |
| CAQ | CG2 | VAL- 18 | 4.12 | 0 | Hydrophobic |
| CAZ | CB | ALA- 31 | 4.03 | 0 | Hydrophobic |
| CBA | CG | LYS- 33 | 3.59 | 0 | Hydrophobic |
| CAY | CG1 | VAL- 64 | 4.28 | 0 | Hydrophobic |
| CAZ | CD1 | PHE- 80 | 3.87 | 0 | Hydrophobic |
| NAO | N | LEU- 83 | 3.38 | 177.57 | H-Bond (Protein Donor) |
| NAJ | O | LEU- 83 | 2.82 | 160.24 | H-Bond (Ligand Donor) |
| DuAr | NZ | LYS- 89 | 3.96 | 137.91 | Pi/Cation |
| CAI | CB | ASN- 132 | 3.64 | 0 | Hydrophobic |
| CAY | CD1 | LEU- 134 | 3.77 | 0 | Hydrophobic |
| CAI | CB | ALA- 144 | 4.18 | 0 | Hydrophobic |
| CAY | CB | ALA- 144 | 3.63 | 0 | Hydrophobic |
