sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.350 Å
X-ray
2003-09-10
| Name: | Cyclin-dependent-like kinase 5 |
|---|---|
| ID: | CDK5_HUMAN |
| AC: | Q00535 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.7.11.1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 41.250 |
|---|---|
| Number of residues: | 22 |
| Including | |
| Standard Amino Acids: | 22 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.530 | 432.000 |
| % Hydrophobic | % Polar |
|---|---|
| 56.25 | 43.75 |
| According to VolSite | |
| HET Code: | IXM |
|---|---|
| Formula: | C16H11N3O2 |
| Molecular weight: | 277.277 g/mol |
| DrugBank ID: | DB02052 |
| Buried Surface Area: | 68.68 % |
| Polar Surface area: | 73.72 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 3 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 0 |
| X | Y | Z |
|---|---|---|
| 39.2719 | 16.3771 | 31.6431 |
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 |
| C11 | CG2 | ILE- 10 | 3.98 | 0 | Hydrophobic |
| C3 | CD1 | ILE- 10 | 3.76 | 0 | Hydrophobic |
| C9 | CG2 | ILE- 10 | 4.19 | 0 | Hydrophobic |
| C18 | CG1 | VAL- 18 | 4.05 | 0 | Hydrophobic |
| C22 | CG2 | VAL- 18 | 4.21 | 0 | Hydrophobic |
| C19 | CG2 | VAL- 64 | 3.84 | 0 | Hydrophobic |
| C19 | CB | PHE- 80 | 3.7 | 0 | Hydrophobic |
| N16 | O | GLU- 81 | 2.86 | 167.81 | H-Bond (Ligand Donor) |
| N4 | O | CYS- 83 | 3.11 | 126.77 | H-Bond (Ligand Donor) |
| O23 | N | CYS- 83 | 2.87 | 165.69 | H-Bond (Protein Donor) |
| C7 | CB | GLN- 85 | 4.08 | 0 | Hydrophobic |
| C11 | CB | ASP- 86 | 3.89 | 0 | Hydrophobic |
| C7 | CD | LYS- 89 | 4.05 | 0 | Hydrophobic |
| C18 | CD1 | LEU- 133 | 3.61 | 0 | Hydrophobic |
| C19 | CD1 | LEU- 133 | 4.06 | 0 | Hydrophobic |
| C22 | CD2 | LEU- 133 | 4.08 | 0 | Hydrophobic |
| C21 | CB | ALA- 143 | 4.02 | 0 | Hydrophobic |
