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
2012-01-31
| Name: | Cyclin-dependent kinase-like 1 |
|---|---|
| ID: | CDKL1_HUMAN |
| AC: | Q00532 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 64.610 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.239 | 698.625 |
| % Hydrophobic | % Polar |
|---|---|
| 55.56 | 44.44 |
| According to VolSite | |
| HET Code: | D15 |
|---|---|
| Formula: | C24H23ClN5O2 |
| Molecular weight: | 448.925 g/mol |
| DrugBank ID: | DB07608 |
| Buried Surface Area: | 59.87 % |
| Polar Surface area: | 114.51 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 4 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 9.87041 | 119.006 | 10.0155 |
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 |
| CAP | CG2 | ILE- 10 | 4.34 | 0 | Hydrophobic |
| CBA | CG2 | ILE- 10 | 4.11 | 0 | Hydrophobic |
| CAP | CG1 | VAL- 18 | 4.32 | 0 | Hydrophobic |
| CBF | CG2 | VAL- 18 | 4.5 | 0 | Hydrophobic |
| CAY | CG2 | VAL- 18 | 3.71 | 0 | Hydrophobic |
| CBD | CB | ALA- 31 | 3.51 | 0 | Hydrophobic |
| CAO | CD | LYS- 33 | 4.48 | 0 | Hydrophobic |
| CAY | CG | LYS- 33 | 4.48 | 0 | Hydrophobic |
| CL1 | CD | LYS- 33 | 3.77 | 0 | Hydrophobic |
| CAN | CG2 | VAL- 64 | 3.9 | 0 | Hydrophobic |
| CAN | CB | PHE- 80 | 3.65 | 0 | Hydrophobic |
| NAV | O | GLU- 81 | 2.7 | 161.31 | H-Bond (Ligand Donor) |
| NAS | N | CYS- 83 | 2.86 | 154.53 | H-Bond (Protein Donor) |
| CAJ | CG2 | THR- 86 | 3.85 | 0 | Hydrophobic |
| NAA | OD1 | ASN- 131 | 2.69 | 168.97 | H-Bond (Ligand Donor) |
| CBD | CD1 | LEU- 133 | 3.64 | 0 | Hydrophobic |
| CAR | SG | CYS- 143 | 4.12 | 0 | Hydrophobic |
| CAM | CB | CYS- 143 | 4.48 | 0 | Hydrophobic |
| NAA | OD1 | ASP- 144 | 3.99 | 0 | Ionic (Ligand Cationic) |
| NAA | OD2 | ASP- 144 | 3.41 | 0 | Ionic (Ligand Cationic) |
| NAA | OD2 | ASP- 144 | 3.41 | 145.55 | H-Bond (Ligand Donor) |
