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
2012-04-09
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.960 | 6.960 | 6.960 | 0.000 | 6.960 | 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: | 31.932 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.581 | 729.000 |
| % Hydrophobic | % Polar |
|---|---|
| 42.59 | 57.41 |
| According to VolSite | |
| HET Code: | 16K |
|---|---|
| Formula: | C15H13N5O2S |
| Molecular weight: | 327.361 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 65.4 % |
| Polar Surface area: | 124.76 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 1 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 1.20509 | -7.13422 | -27.2933 |
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 |
| C9 | CB | ILE- 10 | 3.99 | 0 | Hydrophobic |
| C6 | CD1 | ILE- 10 | 3.61 | 0 | Hydrophobic |
| S | CG2 | VAL- 18 | 4.44 | 0 | Hydrophobic |
| C14 | CG2 | VAL- 18 | 4.41 | 0 | Hydrophobic |
| C5 | CB | ALA- 31 | 3.7 | 0 | Hydrophobic |
| C5 | CG1 | VAL- 64 | 3.94 | 0 | Hydrophobic |
| C5 | CB | PHE- 80 | 4.35 | 0 | Hydrophobic |
| C15 | CD2 | PHE- 80 | 3.51 | 0 | Hydrophobic |
| N2 | N | LEU- 83 | 3.02 | 168.99 | H-Bond (Protein Donor) |
| N3 | O | LEU- 83 | 2.78 | 157.84 | H-Bond (Ligand Donor) |
| C14 | CB | ASN- 132 | 4.32 | 0 | Hydrophobic |
| S | CD2 | LEU- 134 | 4.21 | 0 | Hydrophobic |
| C5 | CG | LEU- 134 | 4.23 | 0 | Hydrophobic |
| C6 | CD1 | LEU- 134 | 3.75 | 0 | Hydrophobic |
| C15 | CB | ALA- 144 | 4.12 | 0 | Hydrophobic |
