sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.200 Å
X-ray
2003-09-10
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 5.700 | 5.710 | 5.710 | 0.010 | 5.720 | 2 |
| 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: | 24.818 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.818 | 529.875 |
| % Hydrophobic | % Polar |
|---|---|
| 50.96 | 49.04 |
| According to VolSite | |
| HET Code: | RRC |
|---|---|
| Formula: | C19H26N6O |
| Molecular weight: | 354.449 g/mol |
| DrugBank ID: | DB06195 |
| Buried Surface Area: | 66.4 % |
| 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 |
|---|---|---|
| 59.6262 | 28.9702 | 26.8357 |
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 |
| CAC | CG1 | ILE- 10 | 3.73 | 0 | Hydrophobic |
| CAI | CG2 | ILE- 10 | 4.21 | 0 | Hydrophobic |
| CAF | CG2 | ILE- 10 | 3.76 | 0 | Hydrophobic |
| CAI | CG2 | VAL- 18 | 3.59 | 0 | Hydrophobic |
| CBA | CG1 | VAL- 18 | 4 | 0 | Hydrophobic |
| CBA | CB | ALA- 31 | 3.72 | 0 | Hydrophobic |
| CBA | CD | LYS- 33 | 4.18 | 0 | Hydrophobic |
| CAY | CG2 | VAL- 64 | 3.61 | 0 | Hydrophobic |
| CAZ | CG | PHE- 80 | 4.31 | 0 | Hydrophobic |
| CAY | CD2 | PHE- 80 | 3.9 | 0 | Hydrophobic |
| CBA | CD1 | PHE- 80 | 3.41 | 0 | Hydrophobic |
| NAO | N | CYS- 83 | 3.25 | 160.22 | H-Bond (Protein Donor) |
| NAJ | O | CYS- 83 | 2.81 | 141.89 | H-Bond (Ligand Donor) |
| CAH | CD | LYS- 89 | 4.3 | 0 | Hydrophobic |
| OAP | O | GLN- 130 | 2.83 | 171.34 | H-Bond (Ligand Donor) |
| CAD | CD2 | LEU- 133 | 4.3 | 0 | Hydrophobic |
| CAY | CD1 | LEU- 133 | 4.01 | 0 | Hydrophobic |
| CAY | CB | ALA- 143 | 4.24 | 0 | Hydrophobic |
